In a low voltage DC (LVDC) distribution system, isolated bi-directional DC-DC converters are key devices to control power flows. A three-phase dual-active-bridge (3P-DAB) converter is one of the suitable candidates due to inherent soft-switching capability, low conduction loss, and high-power density. However, the 3P-DAB converter requires a well-designed controller due to the influence of the equivalent series resistance (ESR) of an output filter capacitor, degrading the performance of the 3P-DAB converter in terms of high-frequency noise. Unfortunately, there is little research that considers the practical design methodology of the 3P-DAB converter’s controller because of its complexity. In this paper, the influence of the ESR on the 3P-DAB converter is presented. Additionally, the generalized average small-signal model (SSM) of the 3P-DAB converter including the ESR of the capacitive output filter is presented. Based on this model, an extended small-signal model and appropriate controller design guide, and performance comparison are presented based on the frequency domain analysis. Finally, experimental results verify the validity of the proposed controller using a 25 kW prototype 3P-DAB converter.