Salary can be shared in many cost centre according to Employee movement by days? is any HR system have the ability to do that automatically?

Yes, this is very much possible to allocate the cost to multiple cost center. 

Under my supervision, i have develop the module where we can put the % of cost & while posting it to finance the cost will automatically get posted to various GL code.

Before i took the charge in this company, accounting we doing manual JV every month to allocated this cost from 1 cost center to another.

I didn't % cost center, I meant employee cost calculated based on the number of actual days that he/she transferred from potion to anther during the payroll month and many  times of transfer in the same payroll month.