The GaN-based critical conduction mode(CRM) totem-pole power factor correction(PFC) converter is a promising candidate for high-efficiency rectifier. When the EMI filter is connected, the grid side current will have low-frequency resonance at the zero-crossing point, which will worsen the THD of the current. This paper analyzes the causes of this problem, and puts forward a solution based on controlling the average value of inductor current. The proposed solution is only realized from the control, which will not increase the hardware cost and is easy to implement. A prototype is built to verify the effectiveness of the scheme.