Unconventional oil and gas, represented by shale gas and shale oil, have occupied an important position in global energy. The rapid growth of shale gas and shale oil production shows great potential for the exploration and development of shale resources. Junggar basin, the main oil-bearing basin in China, is rich in oil and gas resources, so it is of great practical significance to carry out systematic research on the geological characteristics of shale reservoirs in this region. To this end, this paper designates the shale reservoir of Pingdiquan Formation in Huoshaoshan area of the Jungar Basin as the research object, carries out a geological survey in that area, analyzes reservoir forming conditions using the geological interpretation method, analyzes different local trap reservoir types and their main control factors by dissecting the explored reservoir, optimizes and evaluates favorable traps using the source, fault, facies and circle coupling analysis method, establishes single good identification standard of sedimentary microfacies, and carries out well-connected sedimentary microfacies analysis. Using geochemical methods, such as rock pyrolysis, maceral analysis, vitrinite reflectance, kerogen carbon isotope, saturated hydrocarbon chromatography, etc., the abundance and types of organic matter of shale in different intervals are analyzed and the geological characteristics of shale reservoirs are evaluated. This paper aims to analyze the oil and gas content of the shale reservoir in Pingdiquan Formation in the Junggar Basin to provide reliable reservoir evaluation and guide better development of shale oil and gas resources in the future. The innovative expenditure of this paper lies in conducting the research from two aspects: the analysis of the main controlling factors of reservoir formation from the structural point of view and the analysis of the pore structure and geochemical characteristics of shale from the core experiment point of view, and also the classification of organic matter, so as to provide a basis for finding favorable traps. The results show that the shale sedimentary system in the study area is a small fluvial delta, which belongs to a compression structure, with developed NNE-oriented structural belts and faults; the structural form is a short-axis anticline as a whole, forming a structural coil closure at −900 m, with a trap area of 50 km2 and a closure height of 180 m. According to the geological interpretation method, 19 faults of all levels were found in the area and the vertical migration conditions of oil and gas were good. Pingdiquan Formation was oil-bearing, with many vertical oil-bearing strata and strong horizontal independence of the reservoir. The sedimentary thickness of the Permian Pingdiquan Formation in the study area is 300~1200 m and the oil-bearing strata are divided into 3 oil-bearing formations, 9 sublayers, and 22 monolayers from top to bottom. The abundance of organic matter in different strata is generally high, with an average total organic carbon content of 3.53%, an average hydrocarbon generation potential of 18.1 mg/g, an average chloroform asphalt content of 0.57%, and an average total hydrocarbon content of 3011 μg/g, all of which belong to the shale standard, especially Ping-2. The organic matter in different layers belongs to types I-II1, and the organic matter types are I-II1, I-II2, and II1-II2, respectively. The average carbon isotope of shale kerogen is −2.4%, which belongs to type II2 kerogen.