Oil and gas reservoir fracture is not only the important reservoir space, but also the main passage of the oil and gas migration. Therefore, the characterization of fracture is of great importance. However, reservoir rocks have strong heterogeneity, how to characterize heterogeneous reservoir fracture accurately is an urgent problem to be solved. Microscopic infrared spectroscopy imaging technique can be used to analyze spectral curve of the mineral molecules, different peak characteristics were got, and rock medium composition, the size of the rock fracture, and fracture filler properties and other characteristics were obtained accurately. In this work, carbonate heterogeneous reservoir of Renqiu buried hill was taken as an example, based on the microscopic infrared spectroscopy imaging technique, by the analysis of core sample infrared imaging spectrogram and spectral curves of different characteristic regions, the physicochemical characteristics of the target sample and spatial distribution of the rock medium were obtained, the regions where rock fracture maybe occurred were predicted and the effectiveness of the fractures was analyzed. The results show that the main medium of rock sample is dolomite. The rock fractures contain hydrocarbon organic and salt-water inclusion, which mainly exist in dolomite medium. The proportion of salt-water inclusion is 51.7%, and that of alkane organic matter is 26.0% in the fracture filler. The fracutres extend from the upper left region of core sample to the lower right region, which shows that the extended region of the core sample may be the passage of fluid migration. The salt-water inclusions can impede the migration of oil and gas, resulting in the decrease of fractures permeability. The experimental results show that the width of fractures is 1～1.5 mm, which belongs to large fracture, oil and gas can pass the fractures smoothly, therefore, the effectiveness of the fracture is good. The results showed that it is feasible to characterize the fracture of heterogeneous reservoir by means of microscopic infrared spectroscopy imaging technique, and it provides a new method for the accurate characterization of the fracture of heterogeneous reservoir.