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The Yingshan Formation in Lower Ordovician is an important hydrocarbon reservoir of the Tarim Basin, northwest China; however, the factors controlling reservoir development in the formation are not fully understood. Data from thin-section observations, scanning electron microscopy, and gamma-ray logging were applied to produce a fourth-order sequence stratigraphic framework for the Yingshan Formation in the Yubei area of the Tarim Basin. The framework was assessed in terms of the carbonate diagenesis of the reservoir rock. The influence of diagenesis on reservoir porosity, the factors restricting reservoir quality, and the significance of the results for exploration are discussed. Diagenesis, dolomitization, and cementation by atmospheric fresh water occurred in the lowstand systems tracts. The sediments in the transgressive systems tract were consolidated by seawater, or dolomitization occurred in the landward mixed zone, or the sediments quickly entered the shallow burial marine diagenetic environment and became compacted. The highstand systems tract experienced significant diagenesis, with seafloor cementation, atmospheric water dissolution and dolomitization. These factors were related to sea-level fluctuation and sedimentary features. The porosity of some high-frequency sequences in the lower part of the Yingshan Formation was improved significantly. In the Yubei area, cementation of the middle part of the fourth-order sequence during burial reduced the porosity and permeability of the reservoir. This was the main cause of reservoir deterioration. During oil and gas exploration, attention should be paid to the higher degree of dissolution in the middle part of the fourth-order sequence and the superposition of atmospheric fresh-water dissolution in the upper part of the sequence.