Inorganic fertilizers and organic manures have been widely used to maintain crop yields. Leguminous green manures are usually used in the paddy fields in southern China. But the effect of green manures or combination of green manures with other fertilizers on soil physical properties, especially soil pore structure, is unclear. Based on a 34-year field experiment, we investigated the effects of different fertilization strategies on soil structural properties of a paddy soil. Four treatments were selected: no amendment as a control (CK), inorganic fertilization of N, P and K (NPK), combined application of inorganic fertilizers and green manure (GM), and combined application of inorganic fertilizers, green manure and swine manure (GSM). Results showed that relative to the CK treatment, the NPK, GM and GSM treatments increased SOC content by 7.9 %, 17.8 % and 25.7 %, respectively (P < 0.05). The increase of SOC content led to increased aggregate water stability in the GSM treatment (P < 0.05) but not in the GM and NPK treatments (P > 0.05). Consistent with SOC, soil bulk density was reduced by 5.6 %, 7.4 % and 17.6 %, respectively, for the NPK, GM and GSM treatments (P < 0.05). Total porosity was significantly increased in all the fertilized treatments (P < 0.05). Detailed pore size distribution analysis revealed that the NPK treatment mainly increased < 25 μm pores (total porosity minus porosity of pores that are > 25 μm), while the GM and GSM treatments mainly increased > 25 μm pores. The GSM treatment also significantly increased the connectivity and fractal dimension of macropores (P < 0.05). The penetration resistance of the paddy soil was not affected by the different fertilization strategies, with a low (< 0.4 MPa) value at the plough layer (0−15 cm) and a high value (up to 1.6 MPa) at the plough pan (15−25 cm). Overall, this study indicated that inorganic fertilizers had beneficial, but limited effects on paddy soil structure. Green manure and swine manure can further improve soil pore structure and soil aggregation.