Three reference letters, two academic and one professional
A professional letter is fine. It can focus on your personality, your characteristics, your leadership, and your willingness to do hard works. All of those are highly valued by a PhD program. It would be even better if you've led some research projects under his supervision or leadership.
It would be even better better (double betters) that he assures your ability of seeking funding or other research supports (such as data, instruments, and manpower) from the industry.
However, if he cannot say those things, I would like to suggest you to find a professor in one of your seminar course or project course that you did a small research project in that course.