The response of flames’ heat release to acoustic excitation is a critical factor for understanding combustion instability. In the present work, the nonlinear heat release response of a methane–air non-premixed flame to low-frequency acoustic excitations is experimentally investigated. The flame describing function (FDF) was measured based on the overall CH* chemiluminescence intensity and the velocity fluctuations obtained by the two-microphone method. The CH* chemiluminescence and schlieren images were analyzed for revealing the mechanism of nonlinear response. The excitation frequency ranges from 10 Hz to 120 Hz. The forced relative velocity fluctuation amplitude ranges from 0.10 to 0.50. The corresponding flame Strouhal number (Stf) ranges from 0.43 to 4.67. The study has shown that the flame length responds more sensitively to changes in excitation amplitude when subjected to relatively high-frequency excitations. The normalized flame length (Lf/D) decreases from 3.79 to 2.37 with the increase in excitation amplitude at an excitation frequency of 100 Hz. The number of oscillation zones along the flame increases with increasing excitation frequency, which is consistent with the increase in the Stf. The low-pass filtering characteristic of FDF is caused by the dispersion of multiple oscillation zones, as well as the cancellation effect of the adjacent oscillation zones under relatively high-frequency excitation. The main mechanism for the local gain peak and valley is the cancellation effect of positive and negative oscillation zones with various Stf. When two adjacent oscillation regions have similar amplitudes, the overall phase-lag becomes more sensitive to changes in excitation frequency and amplitude. This sensitivity leads to nonlinear anomalous changes in the phase-lag near the frequency corresponding to the gain valley. The calculated disturbance convection time is consistent with the measured time delay in the short flame scenario. Further research is required to determine whether the identified agreement is a result of the consistent occurrence of the oscillation zone in close proximity to the flame’s center of mass, in conjunction with a precise determination of the average convective velocity.