Experimental studies of soot morphology based on analysis of transmission electron microscopy (TEM) images usually neglect the potential effects of primary particle polydispersity and overlapping. In this study, fractal aggregates of different sizes consisting of polydisperse and overlapping primary particles were numerically generated using typical fractal dimension and prefactor relevant to soot. A total of 3600 simulated two-dimensional projections for each primary particle size distribution and level of overlapping considered was produced and analyzed using two TEM image analysis methods commonly used in the literature to evaluate the effects of primary particle polydispersity and overlapping on the recovered morphological parameters of soot. Fairly large deviations in the recovered number of primary particles in aggregates were obtained by both methods considered using the procedure commonly used in the literature. A recommendation was proposed to improve the accuracy of the retrieved number of polydisperse primary particles in an aggregate. We show that the results obtained by using both the Tian et al. (2006) and Brasil et al. (1999) methods can be significantly improved by using the recommended modification for primary particle polydispersity levels commonly encountered in flame soot. Finally, we recommend to use the modified Tian et al. 2006 method for recovering the number of primary particles of aggregates consisting of both polydisperse and overlapped primary particles.