The main purpose of this paper is to study the factors that control changes in rock structure during catagenetic transformation of organic matter. Hydrocarbon generation and primary migration can be controlled by numerous parameters; the most important are temperature, pressure, hydrocarbon composition, and organic matter type and content. The influences of most of these parameters have been studied and experimentally demonstrated. However, there are a few works that are dedicated to the investigation of the texture features of rocks, as well as the quantitative content of the organic matter on the pore space transformation of rocks. Therefore, these parameters are the most important when studying the primary migration processes. It was found experimentally that the rock pore space after each stage of heating is transformed, forming new pore spaces and channels that connect the primary pores. A sample with a relatively low content of organic matter has been found to undergo fewer changes in pore-space morphology in comparison to rock that is saturated in organic content. It has been found that that the change of pore-space morphology depends on the original structure of the rocks. Most of the structural changes were observed during rock heating within 260–430°C; the most intense formation of hydrocarbons was revealed within this interval.