Hi,
I currently just got my transcript of master program (UK) except for the final dissertation, which is 59.4 of 100. Obviously, my final master certificate will be a Merit or 2:1 due to the good result of my graduate project.
But I want to continue the phd study in Germany, is this result (a Merit) would affect my phd application compared to other candidates if they have a higher result such as a Distinction?
or my higher motivation to do the phd would gain more possibilities to get the phd position?

The latter. Grades do matter though (otherwise what's the point in trying?). But a merit is great anyway. They'll probably take a whole host of factors into account I reckon - such as your enthusiasm and your proposal, not just your grades.