Forced periodic operation (FPO) has emerged as a promising process intensification strategy for nonlinear catalytic reactors. In this study, the nonlinear frequency response (NFR) methodology was applied to investigate square-wave FPO of an isothermal CSTR for methanol synthesis. The analysis focused on periodic modulation of the inlet CO and flow rate, considering both single-input and simultaneous-input forcing. The reactor response was evaluated using higher-order frequency response functions (FRFs) to quantify the non-periodic component responsible for time-averaged process enhancement. The results showed that individual modulation of either inlet CO or flow rate doesn't provide significant improvement in reactor performance and may even reduce methanol productivity. In contrast, simultaneous modulation of both inputs generates a strong positive nonlinear interaction that substantially enhances reactor performance. Under optimal forcing conditions, methanol productivity increased from 336.9 mmol min⁻¹kgcat-1 at steady-state to 553.6 mmol min⁻¹kgcat-1, corresponding to a 64.3% improvement. Compared with previously reported cosine forcing, square-wave modulation nearly doubled the attainable productivity enhancement while also improving hydrogen utilisation efficiency. The results demonstrate that square-wave FPO represents a highly effective strategy for methanol synthesis intensification and confirm the capability of the NFR methodology for a priori evaluation and optimisation of periodically operated catalytic reactor systems.