In spite of the role of alkali in enhancing oil recovery (EOR), the formation of precipitation during alkaline-surfactant-polymer (ASP) flooding can severely do harm to the stratum of oil reservoirs, which has been observed in situ tests of oil fields such as scale deposits found in oil stratum and at the bottom of oil wells. On the other hand, remarkable variation of stratum parameters, e.g., pore radius, porosity, and permeability due to scale formation considerably affects seepage flow and alkaline flooding process in return. The objective of this study is to firstly examine these mutual influential phenomena and corresponding mechanisms along with EOR during alkaline flooding when the effects of precipitation are no longer negligible. The chemical kinetic theory is applied for the specific fundamental reactions to describe the process of rock dissolution in silica-based reservoirs. The solubility product principle is used to analyze the mechanism of alkali scale formation in flooding. Then a 3D alkaline flooding coupling model accounting for the variation of porosity and permeability is established to quantitatively estimate the impact of alkali scales on reservoir stratum. The reliability of the present model is verified in comparison with indoor experiments and field tests of the Daqing oil field. Then, the numerical simulations on a 1/4 well group in a 5-spot pattern show that the precipitation grows with alkali concentration, temperature, and injection pressure and, thus, reduces reservoir permeability and oil recovery correspondingly. As a result, the selection of alkali with a weak base is preferable in ASP flooding by tradeoff strategy.