Tectonic diagenesis is a common and important geological phenomenon. We can fully understand the diagenesis of compressional basins through studying tectonic diagenesis. In this paper, we presented the tectonic diagenetic characteristics in the Kuqa area of the Tarim Basin by integrated method of geological analysis and paleotectonic stress. The results showed that the Mesozoic-Cenozoic tectonic diagenesis affected sandstone compaction evolution mainly through physical mechanisms. It showed characteristics of abrupt change and nonthermal indicator (it means that sandstone compaction can not be explained by thermal diagenetic compaction alone because actual sandstone compaction was larger than thermal compaction), which were different from the thermal and fluid diagenesis. Compared with thermal diagenesis, tectonic diagenesis had a typical tectonic compaction in very short time, and many phases of tectonic deformation showed multiple abrupt changes of compaction. There are obvious differences between tectonic and thermal diagenetic compaction, leading to sandstone compaction being larger than the thermal compaction under the same thermal evolution stage in the areas where tectonic deformation happened. The stronger the tectonic deformation, the more obvious the difference. Tectonic process changed the stress distribution through changing the tectonic deformation styles, resulting in different tectonic diagenesis effects. Therefore, tectonic diagenesis of Mesozoic-Cenozoic in the Kuqa area can be divided into four types including rigid rock restraint, fault ramp, low angle fault slippage, and napping.