This paper is the result of geological survey engineering. Objective The purpose of this paper is to synthesize the theories and methods of comprehensive geochemistry and high resolution sequence stratigraphy. The high–precision chemical sequence stratigraphic framework of Wufeng Formation and Lower Longmaxi Formation in Xindi 1 Well, Upper Yangtze region was established to provide scientific basis for shale gas exploration in the study area. Methods We use the core, logging and sample analysis data of Well Xindi 1 in Upper Yangtze region to optimize the indicators system which can divide the chemical sequence stratigraphic. The indicators system contains three elements assemblages: the terrigenous input intensity(TII), the autogenetic precipitation intensity(API), and the organic matter adsorption and deoxidation intensity(ODI). Then the fourth–order chemical sequence stratigraphy is divided by these three elements assemblages. Results Based on the above indicators system, Wufeng Formation of Liutang section is divided into LCW sequence, the lower part of Longmaxi Formation is divided into MCL1–1, MCL1–2, MCL1–3, MCL1–4 fourth–order sequences upwardly. The total amount of elements assemblages related to TII is relatively high near the sequence boundary, but relatively low near the maximum oceanic flooding surface. However, the total amount of element assemblages related to API and ODI are generally lower near the sequence boundary and higher near the maximum flooding surface. Conclusions Representing different genetic significance, the cyclic variation of element assemblages is respond to regional sea level change, and has regional consistency. The sedimentary environment with smaller TII, smaller API and larger ODI is conducive to organic matter enrichment in shale. So it can be used as the basis for regional stratigraphic correlation.