How is a Msc thesis judged? I will have to submit my master of science thesis (in the engineering field) in 2 months, therefore I would like to know which aspect of the thesis are taken into account the most in the final evaluation. 

Also, is it mandatory for this kind of thesis to have as output a new procedure/methodology? And what if mine doesn't?

What are the main factors that the commission will focus on when deciding the final evaluation of the work done?
Which aspects are taken into account with an evaluation depends highly on the university and master study. However, to give you some information about the process and evaluation, I can give you an example how this goes at the University of Amsterdam (The Netherlands), at the Faculty of Science:

The final evaluation is done by your supervisor and the second reader. And if you have a thesis defence, you will be evaluated by the supervisor, second reader, and one member of the board of examination. Then we have a list of aspects that will be taken into account. These can be found here (PDF).

I hope this may help you to have more insight in the evaluation. Else, you can also look up some scientific articles for example at Google Scholar. And, depending on what kind of study you are doing, make sure your thesis is in the right format. For Computer Science for example, a thesis needs to be in ACM Format.