A pure component topological index was integrated with the modified Grunberg–Nissan or the modified Dalton-type mass‑average equation to calculate the mean topological index χm,1 or χm,2 of five biodiesel fuels (peanut, canola, coconut, and palm, soybean oil). Then, the χm,1 or χm,2 was respectively related with the SMD values of biodiesel fuels (taken from the literature, at 313 K), and two regression equations were obtained. The regression equation derived from χm,1 has a higher predictive accuracy than the regression equation derived from χm,2, and the deviations of these two regression equations were within 1.73% and 1.87%, respectively. Furthermore, a regression equation derived from the correlation of χm,1 and SMD was used to calculate the SMD values of biodiesel fuels (at 353 K), and the deviations were within 0.78%. Three types of hypothetical biodiesel fuels were investigated to know the effect of the molecular structure (carbon number and unsaturated bond) on the SMD. A suitable material for the preparation of a biodiesel having the comparable atomization with the diesel no.1 or no.2 will be composed of such components (low carbon number and more unsaturated bonds).