Abstract: The Middle Jurassic Toutunhe Formation in the Fudong slope area of the Junggar Basin is a typical reservoir. Many problems such as remaining oil which is hard to extract and low recovery efficiency are found in deep development. To solve these problems, the microscopic heterogeneity in the second member of Toutunhe Formation was studied. In order to describe grain heterogeneity, pore throat heterogeneity and interstitial material heterogeneity, some methods such as mercury injection, X-ray diffraction and scanning electron microscopy were used to investigate microscopic heterogeneity in detail. Within a high resolution sequence stratigraphic framework, the relationship between crucial short-term base level cycle (SSC4 and SSC7) and microscopic heterogeneity are discussed. Through different structures of cycles because of A/S, pore throat heterogeneity induced by grain heterogeneity and interstitial material heterogeneity (especially matrix) affects reservoir microscopic heterogeneity in rising half cycle in SSC4 under the condition of A/S≤1. Pore throat heterogeneity induced by grain heterogeneity and interstitial material heterogeneity (especially cement) affects reservoir microscopic heterogeneity in rising half cycle in SSC4 under the condition of A/S>1. Pore throat heterogeneity induced by grain heterogeneity affects reservoir microscopic heterogeneity in rising half cycle in SSC7. Drift in intensity of microscopic heterogeneity should be noticed when planning development in reservoir sands in different important short-term cycles in order to enhance oil recovery.