Through conducting a 180-day indoor soil incubation experiment, a comprehensive investigation was carried out to explore the influence of size (mm-, μm-, and nm-size) on the physicochemical and microbiological properties changes of farmland soil mediated by polyethylene microplastics (PE-MP). The results demonstrated that, following the 180-day incubation period, all three sizes of PE-MPs significantly improved the stability of soil aggregates, particularly the μm-size PE-MP (μMP). The addition of PE-MP, irrespective of particle sizes, significantly reduced NH⁺₄-N content, with more pronounced reductions observed in the mm-size PE-MP (mMP) and μMP treatments. The NO₃^--N content significantly decreased in the mMP and μMP treatments, while exhibiting insignificant changes in the nm-size PE-MP (nMP) treatment. All three PE-MPs significantly reduced soil pH, with the greatest reduction was observed in the case of nMP. Regarding dissolved organic carbon (DOC) content, a significant increase was observed in the mMP treatment, whereas a marked decrease occurred in the nMP treatment. Furthermore, the additions of PE-MP with different sizes consistently increased the richness and diversity of bacterial community while decreasing the richness and diversity of fungal community. Specifically, the mMP and μMP significantly reduced the relative abundance of microbial taxon associated with unstable carbon utilization (e.g., Proteobacteria), whereas the nMP significantly increased the relative abundance of microbial taxon associated with relatively stable carbon utilization (e.g., Penicillium) and remarkably decreased the relative abundance of microbial taxon associated with nitrogen conversion (e.g., Myxococcota). These findings affirm that the influence of size on PE-MP-mediated soil property changes exhibites significant variations depending on specific indicators, underscoring the necessity for a comprehensive consideration of the trade-offs among the impacts of PE-MP with different particle sizes on various soil properties when assessing the potential environmental risks of PE-MP.