Depletion can induce aggregation of nanoparticles and therefore has been employed for size fractionation of nanoparticle dispersions. In this study, depletion-induced separation of solvophilic nanorods in polymer solution is explored via dissipative particle dynamics. Three possible equilibrium states are observed upon polymer addition: dispersion, pre-transition (formation of clusters), and phase separation. By varying the concentration (φR) and length (L) of nanorods or changing the system temperature (T), two morphological phase diagrams including φR-L and φR-T are obtained at a given polymer concentration. For a binary nanorod mixture in the pre-transition state, the cluster can be homogeneous or mixed and the latter hinders the size fractionation. According to the φR-L phase diagram, two criteria associated with the formation of homogeneous clusters are given. Based on the criteria, two methods, dilution and temperature increment, for the improvement of fractionation resolution are proposed. This methodology can be generally applied to fractionate nanoparticle dispersions of any kind.