So I am ambivalent to choose between UPM, USM and UKM to pursue my PhD. Which one is better based on academic and environment wise?

I'll be pursuing my studies in Medical Biology.

When it comes to PhD, it mainly comes down to choice of supervisor and research area. it's much more different from bachelor where they look at your final grade and transript. I hope you're not applying blindly to the institute and hoping for them to assign a random supervisor to you.

For PhD, people will look at what you have done and your research skills. Each supervisor will have their own field of interest and idea for project. It would be better to approach and talk to them, ask them bout the project as well as their current funding (it is challenging to work on a project with limited funding!).

Then only you make your choice depending on what interest and your view on the working environment (lab, requirements etc).