Saline-alkali lands, characterized by high soil salinity and alkalinity, pose challenges for sustainable agriculture. Crop rotation systems such as rice-wheat are common practices but face stunted yields due to long-term chemical fertilizer applications promoting topsoil caking. Nitrogen-fixing cyanobacteria can replace nitrogen fertilizers but still require phosphorus. Chemical phosphate fertilizers further salinization and phosphate immobilization, underscoring the need for efficient phosphorus utilization. This chapter aims to construct a low-cost cultivation system to efficiently trap phosphorus and nitrogen using cyanobacteria flocs coupled with agricultural wastewater. The chapter also discusses how to improve cyanobacteria to release more phosphorus through plant-microbe interactions to promote stress tolerance in saline-alkali crop fields. Furthermore, to develop a precise application strategy for cyanobacteria biofertilizers during rice-wheat rotations under various climates, this chapter explores optimizing cyanobacteria cultivation, enhancing phosphorus release through plant-microbe interactions, and tailoring application methods to diverse environmental conditions. This approach aims to improve nutrient availability, mitigate soil degradation, and promote sustainable agricultural practices in saline-alkali lands. This will inform global sustainable agriculture policies for saline land management and food security.