A method for controlling well bore pressure based on model prediction control theory and systems theory, includes: detecting a well bottom pressure, a stand pipe pressure, a casing pressure, an injection flow rate and an outlet flow rate during the drilling operation process and determining the presence of overflow or leakage; if there is no overflow or leakage, then fine-adjusting the wellhead casing pressure according to the slight fluctuations of the well bottom pressure, the stand pipe pressure or the casing pressure; if there is overflow or leakage, simulating and calculating the overflow or leakage position and starting time of the overflow or leakage, predicting the variation over a future time period of the well bore pressure in the well drilling process, and utilizing an optimization algorithm to calculate the control parameter under a minimum of an actual well bottom pressure difference during the future period.