The application of GaN power devices has significantly increased the power density of flyback power supplies but has also caused severe electromagnetic interference (EMI) issues. To address the challenge of conducted interference in flyback power supplies, a comprehensive analysis of the transmission mechanism of conducted common-mode noise is undertaken. This analysis involves simplifying the equivalent model of conducted interference and leveraging the circuit characteristics of conducted noise to propose a solution for attenuating common-mode noise. Considering the constraints of external compensation capacitors, a balanced winding is further introduced to mitigate the impact of noise. To enhance the efficacy of conducted interference suppression, it is suggested to change the winding structure of the transformer and incorporate a shielding winding. This configuration aims to minimize the generation and propagation of common-mode noise within the transformer. Finally, experimental verification is carried out using a 150 W GaN flyback power supply prototype. The experimental results demonstrate that the proposed method effectively suppresses common-mode noise in the circuit.