Despite the great success in the global exploration and development of reef reservoirs, research on bioclastic shoals under reefs is still in its infancy. Bioclastic shoal reservoirs are very thin, with multiple vertical levels and fast lateral changes, which makes accurate prediction of the reservoir’s location much tougher. To further implement the reservoir distribution, under the guidance of sequence stratigraphy, the prediction of thin shoals under the control of an isochronous stratigraphic framework was established. Using the combination of spectrum shaping and F-X domain noise suppression techniques and utilizing the signal-to-noise ratio spectrum set as the reference, logging curve as supervision, and well seismic calibration and isochronal amplitude slicing as quality control, the seismic frequency band was extended, and the seismic data resolution and signal-to-noise ratio were improved. After frequency extension, the global optimal seismic automatic interpretation technique was used to construct an isochronal stratigraphic framework model. Through waveform facies-controlled inversion and waveform facies-controlled simulation techniques, the elastic properties of the shoal reservoir were obtained, from which the planar distribution of the reservoir was accurately predicted. The above methods were applied to the prediction of the bioclastic shoal reservoir in the lower submember of the Changxing formation in the Yuanba gas field (China). The plane distribution of bioclastic shoal in the first and second levels was identified, which provides a guideline for the prediction of thin shoal reservoirs.