AbstractGreenhouse vegetable production (GVP) is developing rapidly and farming practices strongly affect soil quality. However, quantitative evidence of the differences in soil macropore structure between organic and conventional greenhouse vegetable cultivation is still unavailable. In this study, we sampled paired organic and conventional greenhouse vegetable soils from the tilled and plough pan layers at sample sites south of Nanjing, China. Using industrial computed tomography (CT) scanning technology to measure soil macropore characteristics, we examined the effects of different farming practices on soil macropore structure, as well as the main factors that influenced soil macropore characteristics. Organic greenhouse vegetable (OGV) production was associated with a greater quantity and quality of soil macropores compared with conventional greenhouse vegetable (CGV) production. The total macroporosity in the tilled soil layer averaged 16.9% in OGV soils, more than twice that of CGV soils. OGV soils exhibited an improved pore size distribution with a greater relative abundance of transmission pores (50–500 μm) and a decreased relative abundance of large macropores (>1,000 μm). Pore size and shape data suggested that OGV soils had fewer soil cracks but more biopores than CGV soils in the tilled layer, as well as more root biopores in the plough pan layer. Furthermore, macropore morphology was improved in both the tilled and plough pan layers of OGV soils. In particular, macropore connectivity was nearly 10 times greater in the tilled layer of OGV soils. Soil organic matter (SOM) content was the dominant factor influencing most macropore characteristics (total macroporosity, connectivity, and relative porosity of 100–1,000 μm pores, all small macropores and elongated medium macropores). We suggest that greater SOM content and consequently better soil macropore structure in OGV soils was dependent not only on greater organic manure input, but also on the non‐application of chemical fertilizer.Highlights Farm management affects soil macropore structure in greenhouse vegetable production. Compared soil macropore structure in organic and conventional greenhouse vegetable cultivation. OGV had greater quantity and quality of soil macropores than CGV. Greater SOM in organic farming contributed to the better soil macropore structure.