The crystallization behavior of polymer nanocomposites is of great significance in scientific level and applications. In this work, the effects of modified filler contents and interfacial interactions on nucleation and crystallization were revealed by Monte Carlo simulation. The results show that the increase of filler content promotes the transformation of nucleation mode and significantly affects the crystallization rate of polymer nanocomposite system. When the modified filler contents in the system are too high, the chain mobility is greatly reduced due to the small spacing of fillers and the strong restriction of grafting points, which limits the diffusion and arrangement of segments to the nucleus and reduces the crystallization rate. By adjusting the interfacial strength between the matrix and modified fillers, it can be found that the nucleation rate of the system is determined by the changes of free energy barrier and diffusion activation energy under different interfacial interactions. In addition, for the polymer nanocomposite system with less fillers or strong interfacial interactions, it is more likely to form edge-on crystals. These results contribute to the design and preparation of high performance polymer nanocomposites.