Bioelectrochemical systems (BESs) hold prospects in wastewater energy and resource recovery. Anode optimization is important for simultaneous enhancement of wastewater energy conversion and effluent quality in BESs. In this study, a multi-physics model coupling fluid flow, organic degradation and electrochemical process was constructed to guide the design and optimization of BES anodes. Based on the multi-physics simulation, spatially-assembled binary carbon anodes composed of three-dimensional carbon mesh skeleton and granular activated carbon were proposed and established. The granular activated carbon conducive to microbe accommodation played a vital role in improving effluent water quality, while the carbon mesh skeleton favoring electron collection and transfer could enhance the bioelectricity output. With an average chemical oxygen demand (COD) removal rate of 0.442 kg m-3 d-1, a maximum power density of 20.6 W m-3 was achieved in the optimized composite anode BES, which was 25% and 154% higher than carbon mesh skeleton BES and granular activated carbon BES. Electroactive bacteria were enriched in composite anodes and performed important functions related to microbial metabolism and energy production. The spatially-assembled binary carbon anode with low carbon mesh packing density was more cost-effective with a daily energy output per anode cost of 221 J d-1 RMB-1. This study not only provides a cost-efficient alternative anode to simultaneously improve organic degradation and power generation performance, but also demonstrates the potential of multi-physics simulation in offering theoretical support and prediction for BES configuration design as well as optimization.