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Compared with traditional microbial fuel cells, the microfluidic microbial fuel cells have higher performance and energy efficiency due to their co-laminar flow characteristic and micro-scale structure. However, there are very few numerical studies on microfluidic microbial fuel cells, which makes it difficult to study the operating mechanism. In this study, a three-dimensional numerical model is developed to characterize and predict the comprehensive performance of a biofilm-based Y-typed microfluidic microbial fuel cell. Multiple physical fields, containing the bioelectrochemical reaction kinetics, mass transport, hydrodynamics and thermal equilibrium, are coupled in this model to investigate the effects of various parameters on cell performance. The model reliability is validated through the previous experiment. Simulation results reveal the non-linear performance trend of microfluidic microbial fuel cells with the augment of temperature. In addition, high fuel concentration can cause the substrate inhibition phenomenon and affect bacterial activity. Model applicability for different parametric analyses is emphasized by exploring the effect of ionic strength on cell performance. Finally, considering the catholyte diffusion, optimization strategies for energy efficiency are presented. The proposed numerical model can be helpful for the experimental guidance and optimal design of microfluidic microbial fuel cells. [Display omitted] • The first three-dimensional model for microfluidic microbial fuel cell is proposed. • Hydrodynamics and thermal equilibrium are coupled together. • Effects of temperature on anode reaction and catholyte property are considered. • Fuel utilization and exergy efficiency are introduced to evaluate performances. [ABSTRACT FROM AUTHOR]