Although the Lissajous frequency modulated (LFM) mode can improve the long-term and temperature stability of the scale factor (SF) for mode mismatch MEMS gyroscopes, its SF nonlinearity poses a significant limitation for full-scale accuracy maintenance. This paper examines the interaction effects among stiffness coupling, system phase delay, readout demodulation phase shift, and velocity amplitude mismatch within the control process. Based on the completion of frequency difference control and demodulation phase matching, we clarify that the remaining stiffness coupling and residual system phase error are the primary factors influencing SF nonlinearity. Furthermore, SF nonlinearity is reduced through error compensation. On one hand, this paper suppresses stiffness coupling through the observation of the instantaneous frequency difference and the application of the quadrature voltage. On the other hand, system phase error is compensated by observing the amplitude control force and tuning the reference in the Phase-Locked Loops (PLLs). Subsequent simulations of these methods demonstrated a remarkable 97% reduction in SF nonlinearity within the measurement range of ±500°/s. In addition, an observed rule dictates that maintaining a sufficiently large frequency split effectively constrains the SF nonlinearity.