To explore the effects of long-term organic and mineral fertilization practices on the physical properties in Ultisol of south China, a study was conducted since 1998 to investigate the effects of a control (CK), application of chemical fertilizers (NPK), application of organic manure (OM), and NPK fertilizer plus straw returning (NPK + straw). Results showed that OM significantly increased soil water retention capacity at all tensions but with larger increment in low tension at depths of 0–10 cm and 10–20 cm (p < 0.05) when compared with the CK. On the contrary, NPK and NPK + straw led to a decrease in soil water retention capacity under chemical treatments. In the field both in wet and dry periods, soil water content was significantly higher in OM than in NPK + straw and NPK (p < 0.05) since soil hydraulic conductivity (saturated and unsaturated) are lower in OM than in other treatments (p < 0.05). OM was also found to have the lowest soil bulk density and penetration resistance of the four treatments. A high negative correlation was observed between the soil organic carbon and the bulk density and the penetration resistance (p < 0.01). In this way, the application of OM improved the clayey soil physical properties.