I am an undergraduate student and have a plan to apply to a master's program.
I am about to start to work on my graduation thesis for graduation at my university.
Question: How does my graduation thesis will affect applying to master's program?
It has, typically, no harmful effect.
In most cases, you will declare the title of the thesis within your CV, or upon request of either potential supervisor or admission committee. Furthermore, as your current advisor would, supposedly, be among your referenvces, she might talk about it within addressing your applied effort onto the thesis progression, probablely.
As you notice, required pointers to the thesis will be taken into account, even without its completion, within your application.