Abstract: The Jurassic coal-measure source rocks in the Junggar Basin have drawn considerable attention in recent years. In our hydrocarbon thermal simulation experiments of these rocks, we found that the dark mudstone evaluated as good source rock, had a much lower hydrocarbon generation capacity than the coal and carbonaceous mudstone, evaluated as poor source rock. Based on this background, we performed Fourier transform infrared spectroscopy (FTIR) and combined the results of semi‒open thermal simulation experiments to explore the association between the molecular structure and hydrocarbon production capacity, with the aim of obtaining a new understanding of hydrocarbon potential of Jurassic coal‒measure source rocks from the perspective of molecular structure. The results indicate that coals exhibit lower condensation of aromatic structures and higher relative abundance of aliphatic structures with a higher degree of branched chaining than mudstones and carbonaceous mudstones. Apparent aromaticity (fa), aromatic abundance parameter I, and degree of condensation (DOC) are negatively correlated with organic matter abundance. The aliphatic structural parameter H demonstrates a substantial positive correlation with organic matter abundance. Furthermore, aliphatic relative abundance factor A is associated with the type of organic matter; the better is the type of the organic matter, the larger is the A value. The combination of the molecular structures with the thermal simulation results shows that the aliphatic hydrogen enrichment of selected carbonaceous mudstone is similar to that of coal. However, the relative abundance of the aliphatic group of it is high, and the DOC of the aromatic structure is low, making the hydrocarbon generation base stronger and easier to crack. Thus, the hydrocarbon generation capacity of carbonaceous mudstone is slightly higher than that of coal. Mudstone has low H and I values, and the DOC is high, indicating that its hydrocarbon base is low, so it has low hydrocarbon generation capacity. Therefore, the molecular structure is closely associated with the hydrocarbon potential of coal‒measure source rocks. When evaluating the qualities of coal-measure source rocks, the influence of molecular structure on these rocks should be considered.