Tarim basin is a typical multicycle and multiplex basin, hydrocarbon generation history of Lower Palaeozoic source rock is characterized by secondary hydrocarbon generation. The former study mostly refers to aspects such as principle and regular pattern. Research about the region, regularities of distribution and affecting factors of secondary hydrocarbon generation in a typical basin is relatively fewer. The authors model the tectonothermal evolution and hydrocarbon generation history of typical wells in each structural unit, then discuss the feasibility, periods and characteristics of secondary hydrocarbon generation of the Lower Paleozoic source rock in different structural units. Synthetically analyzing typical wells together with structural evolution and thermal history can make it possible to determine the period and region of secondary hydrocarbon generation. The main regions of secondary hydrocarbon generation of Ordovician source rock are distributed in the Shaya uplift, the middle part of Katake uplift, and the west part of Guchengxu uplift. And for Cambrian strata, they are in Shaya uplift, the middle part of Katake uplift, and Bachu uplift. The difference of secondary hydrocarbon generation in different structural units is that they began in different time. It is the tectono‐thermal evolution that controlled the secondary hydrocarbon generation. Reservoir formation had been affected by secondary hydrocarbon generation.