Mixed matrix membranes (MMMs) have emerged as a promising solution for the treatment of dye wastewater. A key challenge in advancing MMMs is how to effectively integrate two nanofillers with distinct advantages to mitigate the limitations of single‐nanofiller systems. In this study, we present a binary nanofiller strategy, utilizing metal–organic frameworks (MOFs) and covalent organic frameworks (COFs), to fabricate polyvinylidene fluoride (PVDF) based MMMs. By systematically adjusting the mass ratio of ZIF‐8 MOF and TFB‐BD(Me)2 COF, the separation efficiency of membranes for dyes with different charges, capitalizing on the molecular sieving properties of MOFs and the superior compatibility of COFs was evaluated. The optimized membrane demonstrated a rejection of 91.66% for Congo red (CR), along with a water permeance of 641.9 L m−2 h−1 bar−1. This work represents a novel attempt in the design of binary‐nanofiller MMMs, offering new insights into the synergistic effects of hybrid nanofillers in membrane technology.