Organic matter (OM) pores are recognized to be the most important pore type in gas shales in the Ordovician Wufeng-Silurian Longmaxi Formation in the Sichuan Basin, China. However, the effects of the type and origin of organic matter on pore development in OM remain controversial. In this study, detailed scanning electron microscope (SEM) analysis of siliceous shales was conducted for core samples from the Wufeng-Longmaxi Formation, taken from five shale gas wells in the Southeast Sichuan Basin. In addition to bitumen, several types of morphologically distinct organic macerals were identified. Due to the high maturity (vitrinite reflectance (Ro) > 2.2%) and compaction of the sample, confirming the origin of some OM types was difficult. However, each OM type is characterized by distinct pore features: (1) the pores in bitumen are normally well developed, with circular or irregular shapes; (2) spherical kerogen contains uneven pores, with irregular and angular pores at the periphery and few pores in the core; (3) algal fragments may have angular pores, the distribution and structure of which are influenced by the initial structure of the organic matter; (4) bacteria-like aggregates represent the accumulation of numerous microbial granules, and contain residual pores; (5) graptolites are relatively tight and usually have few or no pores. The findings indicate that bitumen and algal fragments are the most favourable hydrocarbon-generating organisms for OM pore development. Notably, organic matter originating from different biological sources can influence the extent, shape, and structure of the pores. Some organic pores are recognized as remained pores of sedimentary stage, which may be previously regarded as pores formed during the gas generation period. •Detailed description of pore characteristics of bitumen and different macerals.•The initial structures of organic matter influence pore shapes, distribution and structure according to SEM analysis.•Some irregular angular pores are recognized to be residual pores formed at sedimentary stage.