To describe the essence of the inter-particle breakage behavior of the granular materials in the cone crusher accurately, an improved model is established based on the inter-particle breakage theory and population balance theory. In this model, a relative particle size ratio is introduced for describing the breakage characteristics of particles with different size, and the transformation of particle shape is considered in the inter-particle breakage. According to the standards of BS 812 part 105, the cubic and flaky particles are selected as breakage materials of inter-particle breakage experiment. Based on the experimental data, the influence of compression ratio, particle size distribution ratio and relative particle size ratio on the inter-particle breakage is investigated, the particle shape transformation function of polynomial form is built, and then the improved inter-particle breakage model considering the transformation of particle shape is established. Thus, the dynamic process of inter-particles breakage with two kinds of particle shapes in the cone crusher is simulated, and the flakiness index of cone crusher product can be calculated theoretically. A full-scale test with ZS200MF cone crusher was conducted in Tangshan, China. The particle size distribution and particle shape component of the crushing product were investigated by simulation with the improved model. Through the comparison of the measurement and the simulation, the maximum error of cumulated weight distribution is 4.8%, and the maximum error of flakiness index is 4.6%, then the effectiveness and practicability of this model are proved. Thus, the improved model can predict the quality of crushing product by utilizing the granular property of feed, the geometry of crushing chamber and operational parameters of cone crusher, which provides a theoretical foundation for product quality improvement, high-energy crushing chamber design and operational parameters optimization of cone crusher.