Parallel vibrating screen could be widely used due to multi-dimensional vibration, which was conducive to efficient screening of particle materials. In order to improve the parallel screening performance, firstly, the three-dimensional parallel vibrating screen with different initial phases model was proposed and the kinematics analysis was carried out. The single factor simulation experiment of initial phase was carried out by EDEM software, then, the simulation results were verified by bench test and the multi-factor orthogonal test was carried out to analyze the influence of each factor on the performance index and get a better combination of factors. The results showed that the experimental results were in good agreement with the simulation results under the same conditions. When the other conditions were constant, as the initial phase angle in X direction was increased, the sieving grain was increased first and then decreased, and the impurity content was higher when the initial phase in X direction was 45°. When the initial phase of in Z direction was 90°, the sieving grain was the lowest, the impurity content was increased first and then decreased with the increase of initial phase in Z direction. The sieving grain was higher when the initial phase were 30° and 60°, the impurity content in the whole sieving time was lower than other levels at 60° and the difference was obvious. The orthogonal test showed that the primary and secondary order of the factors affecting the screening efficiency was X amplitude, Y amplitude, Z initial phase, X initial phase, Y initial phase and Z amplitude. The primary and secondary order of the factors affecting the dirt percentage was Z amplitude, Y amplitude, X amplitude, X initial phase, Z initial phase and Y initial phase. The efficiency of three-dimensional vibration was improved by 62.02% and the inclusion rate was reduced by 53.85% when using the best combination of parameters.