The invention relates to a saturation and free water surface calculation prediction method based on microscopic heterogeneity characterization. The problem that an existing conventional method cannotaccurately calculate the original saturation of an oil reservoir transition zone is mainly solved. The method mainly comprises the following steps: 1) collecting related data of a target oil reservoir; 2) achieving fitting of a Thomeer function curve and a mercury injection curve to obtain microscopic heterogeneity characterization parameters; 3) comparing and analyzing nuclear magnetic data and the like to confirm microscopic pore throat structure characterization parameters; 4) realizing nonlinear regression through deep research of a coring well mercury injection curve sample point, and obtaining a formula for predicting microscopic pore throat structure characterization parameters by using conventional logging information; 5) inputting related data, and iteratively calculating the water saturation and the free water surface depth; and 6) counting and analyzing a prediction result, and carrying out quality control and confirmation on application of the technology. The method can calculate the reservoir saturation and the free water surface depth accurately, and establishes a bridge understanding from microcosmic to macroscopic and understanding from static to dynamic.