The positive significance of promoting and applying microbial fertilizers was summarized. Furthermore, their specific application in crops such as rice, wheat, sweet potato, rape, soybean, and peanut was reviewed. The beneficial microorganisms in microbial fertilizers could decompose organic matter and activate nutrients, thereby improving soil fertility and plant disease resistance. Growth hormones secreted by these microorganisms were shown to promote crop growth and increase yield and quality. Additionally, these microorganisms were capable of degrading pesticides, chemical fertilizers, and heavy metal pollutants while suppressing soil-borne pathogens, thus contributing to the sustainable development of agricultural ecosystems. The application effects of microbial fertilizers were demonstrated in various crops. In rice cultivation, when combined with chemical fertilizers, the number of grains per panicle and 1 000-grain weight were significantly increased, while the germination rate and yield under low temperature conditions were improved. In wheat cultivation, photosynthetic efficiency was enhanced after application, and the incidence of powdery mildew and rust was effectively reduced. In sweet potato cultivation, the contents of starch, protein, and sugar were significantly increased by the application of microbial fertilizers. The germination of rapeseed seeds and the growth of seedlings were promoted when an appropriate amount was applied. In soybean and peanut cultivation, plant height, branch number, pod yield, and quality were significantly improved after the application of microbial fertilizers. This paper provided a reference for the scientific application and promotion of microbial fertilizers to support green and sustainable agricultural development.