Guilin Sun
Ansys Employee

"According to theoretical principles, the Q-factor should be calculated based on the Full Width at Half Maximum (FWHM) of the resonance obtained"

This is only one theory, and it is simplified if you know.

Harvard used Lumerical FDDT to obtain Q over a million in 2008: 

Murray W McCutcheon and Marko Loncar. 2008. “Design of a silicon nitride photonic crystal nanocavity with a Quality factor of one million for coupling to a diamond nanocrystal.” Optics expressOptics Express, 16, Pp. 19136-19145.
 
Please be assured that the method calculating Q from the analysis is theoretically correct. The only thing you need to take care is to make sure the time slot you choose is proper.If you use the log method, make sure the intensity at log scale vs time is a straight line. If you use findresonance, it does not need long simulation neither.