Is my Ph.D. research topic worthy? I am a third-year Ph.D. student in the Industrial Engineering department and my supervisor owns a company based on the technology which I initially intended to work on under his supervision. I am mostly interested in the technical aspects of his work, for example, modifying software and hardware to enhance the capability of the existing method. But my supervisor wants me to work on validation of his product to be clinically approved.

I have already submitted a paper (under review) based on validation of his product and now he wants my whole Ph.D. to be based on validation by preparing more validation papers. I am good with programming and software (my initial interest) but he thinks I am not capable of doing that for the product development. More importantly, he wants me to publish papers on behalf of his product for FDR approval which later I found out his primary purpose. 

With this topic neither can I publish original scientific research work since all my papers will be based on validation of an existing product nor can I gain expertise about any tools or software. Will it worth later if I stick to it and manage to get a Ph.D.?
At some point, if you are to have an academic career, and maybe any career, you are going to have to separate yourself from this advisor. I question his ethics, actually, in keeping you so close to something from which he benefits outside academia. 

If you state correctly that he is only letting you work on less consequential aspects, I doubt that he will offer you great support in the future. This seems like a double dead end. 

But quitting seems like it would be too extreme a step, also cutting off your future career. 

My suggestion would be to explore, quietly, with other faculty, whether you can work with them on a dissertation, perhaps cutting ties with your current advisor or perhaps working jointly on another project that is unrelated, or at least less related, to the current advisor's company. 

It is important to keep your search a bit quiet, if possible, though you can explain your reasoning to other professors, I think. I would first look within your current institution, and if nothing is available, start an external search for an advisor. It may be possible to enter another program as an advanced student, skipping some/many of the requirements that you have already fulfilled. 

There isn't much in doctoral study than having an incompatible or somehow unhelpful advisor. You can, I hope, solve that problem without quitting your studies altogether.