Carbonate sediments are susceptible to many factors, such as paleostructure, diagenesis, and strong microbial alteration; as such, their sedimentary architecture still calls for further research. In this study, the reef and shoal bodies in the XVm and XVp layers of the Middle–Upper Jurassic Karlov-Oxfordian in the S gas field were used as the object, and the architecture of the reef-shoal facies was studied. Based on the idea of “vertical grading and horizontal boundary”, the interface characteristics of the 6th to 4th levels of reef-shoal bodies in the study area were summarized, as were four ways to determine the boundaries of reef-shoal bodies. Based on the dense well network, we quantitatively described the scale of each small layer of single reef shoal body through the point-line-surface method and established a geological database of the reef shoal bodies in the study area. In addition, we established the width and thickness of the reef shoal body and the empirical formula for relationships. The study of morphological characteristics of reef-shoal bodies and the degree of overlap revealed six architecture models of reef-shoal bodies. The vertical and lateral superimposed reefs were obtained by evaluating the reservoir space, pore throat characteristics, and physical property characteristics corresponding to various architecture models. The vertical and lateral superimposed shoals corresponded to large reservoir thicknesses. The petrophysical properties were good, and we concluded that the reef-shoal superimposed area was a sweet spot for reservoir development. We applied the research results of reef-shoal architecture reservoir characteristics to gas field development, and therefore improved well pattern deployment in the reef-shoal superimposed area. By comparing the test results of newly deployed horizontal wells with adjacent vertical wells, we confirmed that the selection of horizontal wells was better for gas field development. This study on the architecture of reef-shoal facies could guide the study of carbonate rock architecture.