Abstract: Microbial fertilizer refers to a group of specific fertilizer products that take use the live activities of probiotics to increase absorption efficiency of plant nutrient, improve plant stress tolerance, suppress soil-borne diseases, and reduce soil pollution factors, thereby reduce soil barriers and improve soil productivity. However, microbial fertilizers exhibit some common shortages in actual practices, such as poor colonization ability, week and unstable effect of probiotics. In order to fit these problems, we summarized the latest research progress in relevant fields worldwide from the aspect of establishing mutual benefits between plant and probiotics, and proposed some perspectives on the innovative pathways of microbial fertilizers, including probiotics screening, nutrient carrier compatibility, synthetic microbial community construction, high-density microbial agent fermentation, and microbial fertilizer application strategies. In detail, 1) screening probiotics that match and benefit to plants with high-throughput and precise technology; 2) providing rhizosphere “prebiotics”, i. e. specific organic nutrients favoriting probiotics to enhance their colonization and function, and building a high-throughput screening technology and system that can intelligently match probiotics and rhizosphere “prebiotics”; 3) constructing a stable synthetic microbial community or isolating a single probiotics with diverse functions to reduce soil multiple barriers; 4) establishing fermenting technologies of organic waste compost containing high-density probiotics; 5) combined applying organic fertilizers in bulk soil and “symbiotics” (a combination of probiotics and prebiotics) in rhizosphere, thereby developing a comprehensive strategy of soil quality improvement and rhizosphere efficiency enhancement. The target is to develop high-quality microbial fertilizers through multidisciplinary and multi-technology integration, which may maintain stable effects in different plant-soil systems.