Being an important type of reservoir in Qaidam Basin, carbonate reservoirs developed widely in the northeast of Qaidam Basin. Based on the field profile survey and samples collection of Lower Palaeozoic in Shihuigou Area of Qaidam Basin, the characteristics and controlling factors of the Lower Paleozoic carbonate reservoirs were studied by means of thin section observation, scanning electron microscopy(SEM) and conventional physical property analysis. The results show that the reservoir primary pore does not develop and the physical property is relatively poor. However, secondary pores such as the dissolution pore, fractures and other type of pore develop. The controlling factors of reservoir properties are selective dissolution, diagenesis and tectonic movement. Through comprehensive analysis of various factors, it is concluded that the pore throat structure of the reservoir is based on the primary pores and reformed by complex diagenesis and the superposition of multi-period tectonism in the later period. The early dissolution is the selective dissolution controlled by the rock fabric, while the crevice produced by the later tectonic movement is the key factor for the development of dissolution reservoir.