Research on the little loligo squid (Uroteuthis chinensis) protein hydrolyzed by papain and Flavourzyme and characterization of hydrolysates was carried out in this article. The optimum hydrolysis conditions of papain were obtained by orthogonal experiments, and the influence factors on the degree of hydrolysis such as enzyme/substrate ratio, hydrolysis time, pH, and temperature were investigated. The effect of Flavourzyme on the degree of hydrolysis was also studied. The characteristics of freeze-dried hydrolysates such as yield, moisture, nitrogen recovery, molecular mass distribution, and amino acid composition were determined. The results showed that papain and Flavourzyme could hydrolyze the little loligo squid protein efficiently, and the degree of hydrolysis was up to 25.82% under the optimum hydrolysis conditions. The average molecular mass of hydrolysates obtained with papain and Flavourzyme was 1,246 Da, and the low molecular mass peptides were the main fraction of hydrolysates. The yield, moisture, and nitrogen recovery of freeze-dried hydrolysates was 19.8, 4.4, and 74.2%, respectively. Compared with suggested patterns of amino acid requirements by the Food and Agriculture Organization of the United Nations/World Health Organization (FAO/WHO), the hydrolysates of the little loligo squid had high nutritional value, and was a potential nutritious supplement used in various food products.