Interactions between starch and nonstarch components have attracted enormous attention, but limited information is available on the interactions between starch and alkaloids. To elucidate the interaction mechanism between Fuzi total alkaloids (FTA) and Fuzi starch, Fuzi starch-FTA complexes with different FTA concentrations (0, 1, 3, and 5 g/100 g Fuzi starch) were prepared, and their structural characteristics, physicochemical properties, and rheological behaviors were investigated. Fourier transform infrared spectroscopy results demonstrated that FTA interact with starch via hydrogen bonding. Moreover, the addition of FTA increased the formation of a short-range ordered structure. X-ray diffraction results confirmed the existence of hydrogen bonding and suggested that the relative crystallinity of Fuzi starch decreases with the presence of FTA. Furthermore, FTA elevated the solubility of Fuzi starch and reduced its swelling power, coagulability, gelatinization temperature, and enthalpy change. Based on rheological analyses, Fuzi starch-FTA complexes exhibited non-Newtonian fluid properties and a typically weak gel rheological behavior. After adding FTA, the shear stress, viscosity, and storage/loss modulus of Fuzi starch decreased. Overall, our work enriches the theory of starch-alkaloid interactions and provides data to support investigation into the future applications of Fuzi starch.