When i did FFT analysis for system i am getting different THD values for a,b,c phases for voltages and currents. Can anyone explain why. Will it be like that? If yes why?
If everything else is ok (constant load, all 3 phases identical and shifted 120° each) your FFT is spanning a time interval that is not an integer multiple of the AC input frequency. This will lead to results resembling an unbalanced behavior as each diode is only conducting within a constant 60° angle (further narrowed by the condition that the input voltage has to be higher than the output voltage).
If the FFT interval does not cover an integer multiple of the AC period this will lead to one or more diode(s) accumulating more on-time than the others - resulting in different THD values.
So it is mandatory to synchronize the FFT with the AC period time !