1. A 3D AF camera module comprising: a first imaging unit for capturing an image of an object from a first angle; a second imaging unit for capturing another image of the object from a second angle different from the first angle; a storage unit for storing the images captured by the first imaging unit and the second imaging unit; a color separation unit for separating the images captured by the first imaging unit and the second imaging unit into red, green and blue colors; a main processor unit electrically connected to the color separation unit, the main processor unit being configured for calculating MTF values of the images and determining a shooting mode of the 3D AF camera module, wherein the shooting mode comprises a first shooting mode and a second shooting mode; an image processing unit electrically connected to the main processor unit and the storage unit, the image processing unit processing the images according to the MTF values calculated by the main processor unit to compensate blurs of each of the images caused by out of focus when the second shooting mode is selected, the storage unit configured for storing the processed images processed by the image processing unit; a first driving unit connected to the main processor unit, the first driving unit driving the first imaging unit to a first focusing position according to the MTF values calculated by the main processor unit when the first shooting mode is selected; a second driving unit connected to the main processor unit, the second driving unit driving the second imaging unit to a second focusing position according to the MTF values calculated by the main processor unit when the first shooting mode is selected, the storage unit configured for storing images captured by the first imaging unit in the first focusing position and the second imaging unit in the second focusing position; and an image combining unit electrically connected to the storage unit and configured for combining the processed images processed by the image processing unit to generate a 3D image or combining the images captured by the first imaging unit in the first focusing position and the second imaging unit in the second focusing position to generate a 3D image; wherein the first imaging unit comprises a first lens module and a first image sensor aligned with the first lens module along an optical axis of the first imaging unit, and the second imaging unit comprises a second lens module and a second image sensor aligned with the second lens module along an optical axis of the second imaging unit; wherein the first image sensor and the second image sensor each comprise a plurality of pixel units arranged in a sensing area thereof, each pixel unit comprises a red pixel, a green pixel and a blue pixel, an image sensed by the first image sensor or the second image sensor comprises a plurality of image portions, each of the image portions corresponds to a pixel unit; wherein the main processor unit comprises: a MTF calculating module configured for calculating MTF values of each image portion of the images; an object distance calculating module configured for calculating an object distance of the object in each image portion of the images according to the MTF values; an object distance judging module configured for determining the shooting mode according to the object distances; a blur calculating module configured for comparing the MTF values of each image portion calculated by the MTF calculating module with corresponding predetermined MTF values, calculating the differences between the MTF values and the predetermined MTF values, and generating blur quantities of each image portion of the images according to the MTF value differences; an offset calculating module configured for calculating offset to compensate a blur of each image portion according to the blur quantities; a focus calculating module configured for calculating the first and second focusing positions of the first lens module and the second lens module according to the object distances of the object in each image portion; and a driving distance calculating module configured for calculating driving distances of the first lens module and the second lens module according to the first and second focusing positions calculated by the focus calculating module.