In order to improve the bioavailability of thiamine and solve the bottleneck problem of its poor stability. Controlled hydrothermal treatment technology had been constructed to achieve stable interactions between starch and thiamine (VB1) molecules, resulting in the preparation of starch-thiamine complexes. The formation mechanism, intermolecular interactions, and structural properties between starch and thiamine were investigated and their digestive and physicochemical properties were explored. FTIR, XRD, ROMAN, and NMR results showed thiamine could interact with starch molecules primarily in two ways. One way was that thiamine could be binded to the exterior of the starch helical cavity via hydrogen bond. The other way is that thiamine could enter the starch helical cavity to form V-type crystals through electrostatic adsorption action, where both interaction ways would exhibit thermal competitive effects. After in vitro gastrointestinal digestion simulation, it was found that following the interaction with thiamine, the content of slowly digestible starch and resistant starch in the starch had both increased. Thiamine could slowly release in the colon, successfully achieving its stable and sustained release, thereby extending its retention time in the human body. Overall, starch-thiamine complexes displayed digestion resistance, encapsulate and protect thiamine, and promote controlled release of thiamine, thereby prolonging its retention in vivo for the fermentation.