The invention discloses a waveform encoding method and system for increasing PWM signal resolution. The method comprises steps of: combining a PWM waveform in m cycles in a first cycle section with a PWM waveform in n cycles in a second cycle section and outputting a combined PWM waveform. The system comprises a PWM waveform generating module, an acquiring module, and a waveform inserting module. According to the method and the system, a common MCU equipped with a hardware PWM module is used for inserting a certain number of front and back duty ratio signal waveforms into implemented duty ratio signals so as to effectively increase resolution. On the premise that the a main clock frequency is not changed and that a PWM signal frequency is not decreased, the method and the system effectively increase the resolution of the PWM signal just by means of a simple algorithm and code-adjusted duty ratio, and saves circuit hardware cost. The method and the system can be widely used in various PWM waveform encoding systems.