Tamarillo is widely grown in Yunnan Province, China, and has been found that it can be used in cheese-making with a distinctive fruity flavour. However, this primary component responsible for curdling milk remains unclear. This study aimed to identify the main component in tamarillo responsible for curdling milk using proteomics and ammonium sulphate (AS) precipitation. Herein, 3199 proteins were identified in tamarillo, of which 546 exhibited hydrolase activity. In particular, a novel serine protease with milk-clotting activity (MCA) and a molecular weight of 79.1 kDa, named “MCP746”, was isolated from tamarillo. The milk-clotting proteases (MCPs) from tamarillo exhibited the highest MCA at 80 °C and stability under incubation temperatures below 70 °C, pH range of 5–8, and NaCl concentrations below 1 mol/L. This study revealed that serine protease is the primary MCPs of tamarillo along with a characterization of its milk-clotting characteristics, providing valuable insights into its potential application in cheese-making.