Carbon isotopes can be used to interpret sea-level changes during deposition, but the accuracy of sea-level changes indicated by shallow-water carbonates remains unclear. We carried out sedimentary microfacies and stable isotope analysis of carbonate rocks in Upper Ordovician Lianglitage Formation in Tazhong area, Tarim Basin, to examine the response of isotopes to high-frequency cycles of shallow-water carbonate rocks. The Lianglitage limestones can be divided into four types of microfacies that were deposited in reef and shoal environments on a platform margin. A total of sixty-one (61) selected limestone samples have the δ13C value varying from 0.5993‰ to 1.6228‰ (average 1.1364‰). The extremely low correlation coefficient of carbon and oxygen isotopes indicate that the samples can represent the deposition seawater, thus the estimated Z value and temperature show that the Lianglitage Formation was deposited in the normal marine environment in a tropical to subtropical zone. The Lianglitage Formation shows a clear deposition trend from tidal flat to reef shoal and then to an open platform. The sedimentary environment controls the difference in carbon and oxygen isotopes of shallow-water carbonates through the rate of burial of organic carbon, and thus the δ13C tend to increase when sea level rise. Hence the carbon isotopic composition of shallow-water carbonate rocks can reflect sea-level changes. The δ13C of Lianglitage Formation in well TZ72 shows four sedimentary cycles (20–40-meters-thick) controlled by sea-level changes, which were also recorded in this Formation from other parts of the Tarim Basin.