The microalgal-bacterial granular sludge (MBGS) process is expected to meet the future requirements of municipal wastewater treatment technology for decontamination, energy consumption, carbon emission and resource recovery. However, little research on the performance of the MBGS process in outdoor treatment was reported. This study investigated the performance of the MBGS system in treating municipal wastewater under natural alternate day and night conditions in late autumn. The results showed that the average removal efficiencies of Chemical oxygen demand (COD), NH₄⁺-N and PO₄³⁻-P on daytime before cooling (stage I, day 1−4) could reach 59.9% ± 6.8%, 78.1% ± 7.9% and 61.5% ± 4.5%, respectively, while the corresponding average removal efficiencies at night were 47.6% ± 8.0%, 56.5% ± 17.9% and 74.2% ± 7.6%, respectively. Due to the dramatic changes in environmental temperature and light intensity, the microbial biomass and system stability was affected with fluctuation in COD and PO₄³⁻-P removal. In addition, the relative abundance of filamentous microorganisms (i.e., Clostridia and Anaerolineae) decreased, while Chlorella maintained a dominant position in the eukaryotic community (i.e., relative abundance > 99%). This study can provide a theoretical basis and technical support for the further engineering application of the MBGS process.