Chinese three-striped box turtle (Cuora trifasciata), as a freshwater turtle, is used as a tonic food. The purpose of this study was to isolate peptides with cancer growth inhibition activity from trypsin-digested hydrolysates of turtle proteins. The results demonstrated that two fractions T1 and T2 exhibited good inhibition on HepG-2 and MCF-7 cancer cells, with an inhibition of 70.65-89.1%, at 500g/mL. Subsequently, three peptides were identified from T1 and T2, including RGVKGPR (T1-1), KLGPKGPR (T1-2), and SSPGPPVH (T2-1). By database search, T2-1 was a completely new peptide; its inhibition activity on MCF-7 cancer cells was the best, up to 70.02% at 500g/mL. Then, T1 and T2-1 were nanoencapsulated by chitosan. After nanoencapsulation, the inhibition percentages were 50.23% for the nanoencapsulated T1 on HepG-2 and 46.82% for the encapsulated T2-1 on MCF-7. The release experiment indicated that the encapsulated peptides could be slowly released in simulated gastrointestinal juice.