It is common method to utilize the geochemical information in carbonate rocks to study the ancient environment and climate changes in the geological history. As in early 1980s, the whole-rock carbonate was studied as main samples. Recently, more attentions has been attracted by brachiopod fossil shells because of their composition which was the low magnesium calcite with high capacity to resist the diagenetic alteration. In this study, the comparison of delta~(18)O, delta~(13)C and ~(87)Sr/~(86)Sr respectively from brachiopod fossil shells and whole carbonate rocks in Longmen mountian in Sichuan province showed: there was higher delta~(18)O values in brachiopod shells, and similar trend in the evolution of ~(87)Sr/~(86)Sr and delta~(13)C between brachiopod fossil shells and the whole rocks carbonate. These results indicated that the geochemical information in the whole rocks carbonate still could be used to as an indicator for reconstructing the evolution of paleoclimate although there were some differences in the geochemical information between the whole rocks carbonate and brachiopod fossil shells, especially in the period within lack of brachiopod fossil shells.