A regulated DC Transformer (RDCX) is usually combined by a DC Transformer (DCX) and a PWM regulator which only processes part of the total power. Thus, it can realize voltage regulation while maintaining high efficiency. However, apart from the common-mode (CM) noise caused by DCX, low-frequency spectrums will also be introduced by the PWM regulator through parasitic capacitors of DCX’s transformer, which makes EMI spectrums more complicated. In this paper, an equivalent circuit of CM noise in cellular RDCX is derived and a winding re-arrangement method is proposed to suppress the CM noise. The equivalent circuit is verified by comparing the calculated results with the measured spectrums. The CM noise is reduced by around 35 dB with the proposed winding arrangement.