Cross-linked enzyme aggregates (CLEAs) have the advantages of high-enzyme activity and stability, and have an application potential in food and feed processing. In order to address the food and feed safety of CLEAs and have ideal enzymatic properties, a new design of CLEAs of lipase from Aspergillus niger is developed by using sodium tripolyphosphate (TPP) as a cross-linking agent and chitosan as an auxiliary agent. The enzyme activity recovery of the developed CLEAs reaches 126%. The half-life of the CLEAs is 11.4-fold higher than that of free enzyme at the optimum reaction temperature of CLEAs. The surface structure of the CLEAs reveals cluster and porous structure. The variations of the secondary structures of the CLEAs indicate an increase of α-helix and decrease of β-sheet, β-turn, and random coil. The adding of chitosan is beneficial to enzyme activity recovery and thermal stability of the CLEAs. TPP and chitosan are safe and nontoxic, and the CLEAs prepared with TPP and chitosan is suitable for the food and feed industries.