To solve the problem of nitrogen loss and harmful gas emissions in the co-composting of cyanobacteria with other wastes and agricultural non-point source pollution in the Chaohu Lake Basin (CHLB), this study selected cyanobacteria as the main material, spent mushroom and rice hulls as excipients, and biochar (B) and Mg2+/PO43− salt as an additive. The nitrogen fixation rate, maturity, toxicity, and fertilizer efficiency indexes were analyzed to explore the best rate of biochar application. Additionally, three different fertilization treatments (C0: No fertilization, CF: Chemical fertilizer, OF: Organic fertilizer) were applied to agricultural field experiments in the CHLB. The results showed that the cyanobacteria composting experiment with 10% B as additives had the lowest cumulative NH3 emission (603.00 g) and the highest nitrogen fixation rate (61.54%). We used this compost product for maize cultivation in field experiments. The results show that OF treatment can reduce field nutrient loss, and the increase in the rate of soil TN fixation was as follows: OF (18.62%) > CF (10.34%) > C0 (−9.66%). Moreover, the TN and TK losses in runoff were 33.33% and 22.74% lower than CF in farmland runoff. The OF treatment increased the content of crude fat, crude protein, and crude starch by 4.40%, 8.34%, and 2.66% compared with the CF treatment, respectively. Overall, the N, P, and K source agronomic coefficients of cyanobacteria organic fertilizer were 1.424, 1.001, and 1.16, respectively. These results indicated that cyanobacterial organic fertilizer could replace chemical fertilizer to reduce agricultural non-point source pollution and improve maize quality. Meanwhile, the amendment of B and Mg/P salt additives could reduce air pollution and improve the quality of compost products. This study provides a theoretical basis and reference for nitrogen fixation and extension of multiple wastes co-composting field experiments.