What would be the most appropriate measure I should take if I feel that I am failing to submit my MSc thesis within deadline? In February-2016, I have undertaken my thesis. That was the topic proposed by my supervisor on my request. I started to work on the project and finding that I am actually short of various topics/knowledge(theoretical and practical). I still contacted the supervisor and he passed me in my lab and told me to continue the work.

The last date of my thesis submission is 2016–09–15. 

I have been started to have a feeling that I wouldn’t be able to complete the thesis. Coz, my previous knowledge is not sufficient to complete the lab-project and hence the thesis.

What would be the consequence if I am unable to submit the thesis?

What would be the most appropriate measure I should take to save my thesis/career/semester/grade and so on?
The key question that you need to answer is "why".  

If there are serious, unforeseeable circumstances that have effected your ability to progress with your research and/or submit on time (such as illness),  then you should refer to your institution's policy and guidance on applying for an extension, mitigating circumstances etc.  Hopefully these will be considered and you will be granted an extension or a late submission will be accepted without penalty.

Some institutions also accept work-related circumstances as mitigating.

If it's down to poor planning, failing to adhere to your supervisor's advice or meet key milestones, bad luck etc, then, alas, it's unlikely that you will be granted any kind of dispensation to submit late.  Nonetheless, I'd advise you contact your supervisor to let them know the situation in the hope that they will help you unpick the situation.

In all circumstances, I'd suggest you talk to your supervisor as soon as possible or another adviser who might be able to help.

EDIT: Let this be a lesson to future readers - always ask for help sooner rather than later if you find yourself running into trouble and fear missing a deadline.  Two weeks before due date isn't going to cut it.