Green manure coverage not only improves soil conditions and enhances soil fertility but also exerts significant effects on soil fauna diversity and ecosystem service functions. However, studies on the effects of manure-maize intercropping systems during both mulching and non-mulching periods on the trophic structure and functional roles of soil fauna remain limited, particularly in desert agricultural ecosystems. Accordingly, this study was conducted in the Zhangye Oasis, located in the arid region of northwestern China, using trap methods to systematically examine the effects of maize and green manure intercropping on soil fauna communities during both the green manure mulching and non-mulching periods. The results showed that: (1) During the green manure mulching period, the activity densities of macrofauna and mesofauna in maize and green manure intercropping fields were significantly higher than those in monoculture maize fields (P < 0.05). However, during the non-mulching period, the activity density, species richness, and Shannon-Wiener index of mesofauna in monoculture maize fields were significantly higher than in intercropping fields; (2) During the green manure mulching period, the activity density of spiders, predatory insects, herbivorous insects, ants, and springtails in maize and green manure intercropping fields were significantly higher than in monoculture maize fields; (3) During the green manure mulching period, the ratios of spiders to herbivorous insects (S/H), and spiders to other feeding types (S/O) was significantly higher in maize and green manure intercropping fields than in monoculture maize fields. In summary, intercropping maize with green manure significantly enhances soil fauna diversity during the mulching period, particularly enhancing predatory groups and their pest control functions, thus supporting the sustainable development of ecological agriculture in desert regions.