Film mulching changes the soil hydrothermal environment in arid and semi-arid areas, which will inevitably affect the community structure and composition of soil microorganisms. Nevertheless, the changes in the community structure and composition of soil microorganisms under different film mulching period and how does film mulching affects crop yields by influencing soil environment mediated by microorganisms were still unknown. To fill the gaps, a long-term field experiment from 2002 was established including four treatments: (1) no mulching (NM), (2) total film mulching in the fallow period (FT), (3) total film mulching in the growth period (GT), (4) total film mulching in the whole year (WT). The results showed that film mulching in different period decreased the richness and diversity of soil fungal community, decreased the richness of soil bacterial community, but had none influence on the diversity of soil bacterial community, compared with NM. FT, GT, and WT had higher nodes number, edges number, average degree, and average clustering coefficient of fungal co-occurrence networks than NM, while only FT increased the modularity. Soil fungal and bacterial communities were mainly driven by random processes and deterministic processes, respectively. FT and WT significantly increased the grain yield by 37.11 % and 21.32 % than NM (P < 0.05). Furthermore, the partial least squares path modeling showed that soil temperature and soil structure were significantly affected by film mulching or not mulching (P < 0.05), while mulching period primarily influenced the soil structure. In general, film mulching in different period could change soil structure, and at the same time, also affect the characteristics of the microbial communities. Film mulching in the fallow period not only achieved the highest grain yield but also created a complex and stable microbial environment than no mulching. This study had important guiding significance for the selection of wheat mulching period in the Loess Plateau of China and similar climate areas.