Earth pressure coefficient at rest K0 is commonly estimated by empirical equations, which to date has had insufficient accuracy and universality. For better prediction, the investigation on the factors influencing K0 is required. A series of discrete element method (DEM) simulations of oedometer tests are conducted to verify the key factors influencing K0 of granular materials. The influences of initial fabric anisotropy, particle shape, initial void ratio, inter-particle friction angle is investigated. The evolution of microstructure is monitored during the tests to reveal the relationship between the microstructure evolution and K0 values. The results show that the effect of fabric anisotropy exists but is limited. Particle shape, initial void ratio, and inter-particle friction angle all significantly affect the K0 values alone. According to the DEM results, an attempt is made to propose a more reasonable empirical equation in which K0 is a function of relative density, critical state friction angle, and “shape factor”. This new empirical equation has higher accuracy and can consider the effect of particle shape, inspiring the determination of K0 values in practical engineering.