I using Matlab and PSCAD for design active power filter. However, the simulation results for both software is same but the THD value from FFT is different. For PSCAD I getting 3.45% THD but for Matlab is about 10%. May I know why these conditions happen??

 

You'd have to look at what equations they use to calculate the FFT to determine the difference.

 

Another possibility: Are you sure that the simulation results are the same? Exactly the same? Or do they just look close enough visually and it's just a matter of not being able to distinguish the difference between those two levels of distortion?