Controlled by the base level change cycle, the carbonates exposed from the periodically shallowed water body at the top of the high-frequency sequence develops multiple sets of thin reservoirs. Such reservoir identification has always been tricky in the prediction of carbonate reservoirs. Based on the Middle Permian strata from the Sichuan Basin, this paper established a forecasting approach of high-frequency-sequence-controlled carbonate thin reservoir. The steps are as follows: (1) Combine the measured results of samples from the typical outcrops with changes of carbon and oxygen isotopes, thus to construct a division program for the 3rd-order sequence of the Middle Permian strata. (2) Compare the carbon and oxygen isotope changes and the global sea level change trend, determine the controlling factors of the 3rd-order sequences. (3) Carry out spectrum analysis based on the natural gamma energy spectrum logging (ln (Th/K)) curves of Wells Long-17 and Anping-1 to establish a high-frequency sequence framework division program, and then apply the logging curve characteristics to correct the top interface positions of the high-frequency sequences, which is the potential location of carbonate reservoir. The research results suggest that the Middle Permian in the Sichuan Basin can be divided into three 3rd-order sequences, which are PSQ1, PSQ2 and PSQ3 from bottom to top. Among which, PSQ1 is mainly affected by global sea level (GSL) changes, and the changes originated from its tuning curve can be directly applied to the division of high-frequency sequences and reservoir prediction. PSQ2 and PSQ3 are jointly controlled by global sea level changes and regional tectonics. In cope with the influence of regional tectonics, the positions of the four-level sequence interface established according to the tuning curve need to be fully considered, and good results were achieved through systematical correction. This method can effectively reduce the risk of reservoir prediction caused by marine carbonate heterogeneity, and provide scientific foundation for the prediction of high-frequency cyclic reservoirs of platform facies and platform margin subfacies in other marine carbonate sedimentary basins.