According to the data of rock thin-section, porosity and permeability, the characteristics of low permeability reservoir and its genesis of the Jurassic in the Southern Yiqikelike tectonic zone of eastern Kuqe Depression in Tarim Basin are studied. The results show the rock types of Lower Jurassic sandstone reservoirs are mainly litharenites and feldsparthic litharenites, which are characterized by lower compositional maturity and higher textural maturity. The types of reservoir space are mainly secondary porosity-primary porosity in the eastern region and crack-secondary porosity in western region. The reservoir heterogeneity is of severity laterally. Generally, the reservoirs have low porosity, low permeability or particular low porosity and particular low permeability. The quality of reservoirs in Tugeerming area of the eastern region is superior to that of the southern region. The factors controlling the reservoir quality are by petrology, sedimentary environment, diagenesis and cracks. However, the most important factor is the combination of the burial compaction and the structural stress, which results in the particular stoniness of the reservoir compaction in the west area.