Intensive aquaculture’s excessive nitrogen, phosphorus, and methane emissions caused environmental degradation. This study explored how algae-bacteria symbiotic systems (ABSS) enhanced water purification by regulating element cycles. We established a Chlorella pyrenoidosa-Bacillus subtilis symbiotic system. At a 1:1 bacteria-to-algae ratio, chlorophyll a and cell dry weight were highest. C. pyrenoidosa supplied organic acids, carbohydrates, and amino acids to B. subtilis, which reciprocated with amino acids, purines, and vitamins. ABSS significantly reduced total nitrogen, ammonia nitrogen (NH4+-N), nitrite (NO2−-N), nitrate (NO3−-N), phosphate (PO43−-P), total phosphorous, dissolved organic carbon, and chemical oxygen demand in aquaculture water. It reshaped microbial communities and enriched key genus (Limnohabitans, Planktophila, Polaromonas, Methylocystis) and upregulating genes linked to organic phosphate mineralization, methane oxidation, and nitrate reduction. These changes strengthened nitrogen-phosphorus-methane cycle coupling, boosting water purification. ABSS offers an eco-engineering solution for aquaculture pollution by optimizing microbial interactions and nutrient cycling.