Coarsening is a common physical process that occurs in polydisperse two-phase mixture systems, which had been widely studied for decades. However, accurate prediction of the volume fraction dependence of the diffusion-controlled coarsening kinetic process is still very difficult. In this work, by using the atomic-scale phase-field crystal model, we investigated the coarsening kinetics of crystalline nanoparticles in the semi-solid region. The results showed that the details of the atomic-scale nature of particles do not affect the kinetics of coarsening for low solid volume fractions and the coarsening process of the nanoparticles is in agreement with the classical coarsening theory. While, for high solid volume fractions, our simulation results show that the coarsening rates of crystalline particles decrease with the solid volume fraction, which runs counter to the theoretical models based on mean-field theories. By checking the competitive growth process of all the particles, we found the appearance of grain rotation and volume diffusion mechanisms leads to the failure of the classical coarsening models.