Vitamin D3 (VD3) was encapsulated in TGaseOVA–chitosan (COS) composite nanoparticles. Isothermal titration calorimetry was used to explain the hydrophobic interaction between TGaseOVA and VD3 at the molecular level. The 87.7 nm TGaseOVA–COS composite nanoparticles achieved an encapsulation efficiency of 96.34% and loading capacity of 4.68% for 9 μg/ml VD3. An in vitro digestion experiment revealed that TGaseOVA–COS–VD3 composite nanoparticles had good stability in simulated gastric fluid and only 32.67% of the composite nanoparticles were released in simulated intestinal fluid. Meanwhile, sodium dodecyl sulfate polyacrylamide gel electrophoresis confirmed that the composite nanoparticles had a release rate of 100% in simulated intestinal fluid. TGaseOVA–COS–VD3 composite nanoparticles had a VD3 concentration of 8.73 μg/ml after pasteurization, indicating that they provided substantial protection to VD3 during pasteurization. TGaseOVA–COS was subjected to a 1-month simulated shelf life test. High-performance liquid chromatography confirmed that it had a VD3 retention rate of 90%. The concentration-dependent toxicity of VD3 was detected by using Caco-2 cells. VD3 exhibited toxicity at the concentration of 11 μg/ml. Therefore, the embedding dose of 9 μg/ml used in this work was considered a safe dose. TGaseOVA–COS composite nanoparticles have excellent stability and good VD3 slow-release properties. They can be used in concentrated clear beverages and other food and beverage products. Therefore, they have potential for applications in the food and pharmaceutical industries.