O isotopes thermometer has been used to study changing in the paleo-climate for dacades. O isotopes in phosphate from fossils are sensitive to the variation of the paleo-climate. Conodont is one of the best samples for the O isotopes study due to its abundant existence within the marine stratum from Paleozoic to Mesozoic and significance in stratigraphy. Sensitive High Resolution Ion Microprobe (SHRIMP) is capable of doing in-situ O isotopes analysis with the diameter of the ion spots less than 20μm by consuming only very few sample and is characterized by high resolution, sensitivity and precision. In this work, we introduce the analytical methods and measuring instruments established in Beijing SHRIMP IIe-MC center for the in-situ O isotopes analysis on conodont for the first time. The continuous 7 days with 253 spots analysis on the apatite standard Durango yields the mean value of δ18Oapatite=9.78±0.29‰, which is consistent with the reference value of 9.81±0.25‰（Ian Williams , unpublished）. As an example, we also measure the O isotopes of 237 conodont samples from 49 strata from the Permian-Triassic profile in Wenbusangdang, Tibet, with 914 analysis spots, and provide reliable and accurate data on the variation of the paleo-temperature during the mass extinction at the Permian-Triassic boundary.