There is increasing interest in developing quinoa products due to their unique nutritional value. Starch and protein are the primary components in quinoa, and the interaction between them affects the quality of quinoa products. This study extracted the starch and protein from quinoa and simulated the thermal processing of quinoa to investigate the effects of starch on the solubility and structure of quinoa protein isolates during heat treatment. The structure of quinoa protein isolates was characterized by fluorescence spectroscopy, Fourier transform infrared spectroscopy, laser particle size analysis, and scanning electron microscopy. The results showed that starch decreased protein solubility, and the maximum solubility was obtained after heating for 5 min. After starch addition during heat treatment, the surface charge distribution of protein changed, the degree of protein aggregation increased, the particle size of proteins increased, the thermal stability increased, and the β-sheet ratio of the proteins increased, suggesting that the protein structure is more ordered, which is the structural foundation of protein solubility decreasing. The research about the interaction between starch and protein and the effects on the solubility of protein could provide a reference for quinoa products processing.