In this paper, the effects of pilot-stage equivalence ratio on combustion instabilities in a coaxial staged model combustor are investigated using the Wall-Modeled Large Eddy Simulation. The global equivalence ratio is maintained constant, and the Stratification Ratio of the first main-stage and the second main-stage is set to 1; the dynamic mode decomposition and system identification methods are employed to analyze the flame dynamics, velocity, heat release rate modes, and flame transfer function (FTF) of the model combustor under different pilot-stage equivalence ratios. The results show that when the pilot-stage equivalence ratio is 0.6, the oscillation amplitude of heat release rate (HRR) exceeds 7.5% of the global average HRR, and the velocity oscillation and the global HRR oscillation in the combustor are coupled. As the pilot-stage equivalence ratio increases to 0.8, the oscillation amplitude of HRR decreases to 2.5%, and the oscillation of velocity and global HRR in the combustor are decoupled. Furthermore, the maximum value of FTF decreases from 3.5 to below 1 with the increase in the pilot-stage equivalence ratio.