The concept of flexible power electronics substation (FPES) has been applied firstly in the Zhangbei dc distribution network demonstration project. As a multi-port power electronics transformer (PET) with different ac and dc voltage levels, the FPES has adopted a novel topology integrating modular multi-level converter (MMC) and four-winding medium frequency transformer (FWMFT) based multiport dc-dc converter, which can significantly reduce capacitance in each sub-module (SM) of MMC and then save space and cost. In this paper, in order to accelerate speed of electromagnetic transient (EMT) simulation of FPESs based hybrid ac/dc distribution systems, an aver-aged-value model (AVM) has been proposed for efficient and accurate representation of FPES. Assume that all SM capacitor voltages are perfectly balanced in the MMC, the MMC behavior can be modeled using controlled voltage sources based on modulation voltages from control systems. In terms of the averaged current transfer characteristics among the windings of the FWMFT and consider that all multiport dc-dc converters are controlled with same dynamics, a lumped averaged model using controlled current and voltage sources has been developed for these four-port dc-dc converters connected to the upper or lower arms of MMC. The presented FPES AVM model has been tested and validated by comparison with a detailed IGBT-based EMT model. Results show that the AVM is significantly more efficient while maintaining its accuracy in EMT simulation.