Production of chitosan and its derivatives by traditional methods involves the excessive use of a reaction solution comprised of sodium hydroxide and hydrochloric acid. Waste water resulting from this process has limited the application of chitosan as a fertilizer as the process causes serious environmental pollution. Specifically, the resulting waste water contains high levels of dissolved nitrogen and minerals from shrimp shells. In this study, an eco-friendly method was established to produce chitooligosaccharides (COS) with different degrees of deacetylation (DDAs) from shrimp shell waste. At a solid-to-solvent ratio of 1:6, the degree of demineralization was above 90% with the treatment of 30 g·L –1 H 3PO 4, and the degree of deproteinization was above 80% when treated with 30 g·L –1 KOH at 70 °C. Chitosans with different DDAs were obtained by microwave-assisted KOH metathesis and the COS with Mw approximately 1500 Da were then prepared by oxidative degradation. In summary, 33.73 kg H 3PO 4, 12.77 kg, and 241.31 kg KOH were supplied during the processes of demineralization, deproteinization, and deacetylation of 100 kg shrimp shell waste, respectively. The process water was totally recycled, demonstrating that the shrimp shell could be wholly transformed into fertilizer. The entire process created a product with the fractions of N:P 2O 5:K 2O:COS = 7.94:24.44:10.72:18.27. The test on the germination promotion of wheat seeds revealed that the COS with 72.12% DDA significantly promoted germination. This work demonstrated the use of an eco-friendly preparation method of COS with a specific degree of deacetylation that can be applied as a fertilizer.