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Abstract In the context of the continuous development of new energy vehicles, an increasing number of electric vehicles (EVs) are being integrated into microgrids, which impacts the operation of microgrids. It is necessary to analyze the emission scheduling of microgrids connected with EVs to ensure the smooth and reliable operation of microgrids with EV integration. This paper aims to realize optimal microgrid scheduling. This article took the case of EV connection with microgrids through orderly charging and discharging. Firstly, mathematical models for each output unit in the microgrid were established. Then, aiming to minimize both the operational cost and pollution emission treatment cost of the microgrid, an emission dispatch optimization model was developed. The whale optimization algorithm (WOA) was chosen as the solving algorithm, and an improved WOA (IWOA) was obtained by optimizing the original WOA in terms of population initialization and position updating parameters. An example analysis revealed that the IWOA demonstrated superior optimization performance compared to other optimization algorithms. In the scenario of orderly charging and discharging, the EVs discharged during peak hours and charged during off-peak hours to balance the microgrid load. The operating cost obtained through the IWOA was 967.25 yuan, and the pollution emission treatment cost was 241.52 yuan, resulting in a total cost of 1208.77 yuan. These results confirm the reliability of the proposed IWOA in solving the model and its applicability in optimizing microgrids with EV integration.