Cropping systems are thought to alter soil quality in paddy rice fields. This study was conducted to quantify the long-term effects of continuous crop production under different cropping systems with different crop rotations on physical properties of alluvial clay soil in the Mekong Delta, Vietnam. Soil samples were collected from four treatments: (i) traditional intensive rice monoculture with three rice crops per year (R-R-R); (ii) rotation with two rice crops and maize (R-M-R); (iii) rotation with two rice crops and mung bean (R-Mb-R); and (iv) rotation with one rice and two upland crops, mung bean and maize (R-Mb-M). We hypothesized that cropping systems with rotations of upland crops and their temporary beds improve the physical quality of paddy rice soil; hence, they are better options towards sustainable agriculture. Results show an improvement of soil physical quality for systems with two rice crops and one upland crop (R-M-R and R-Mb-R) and those with one rice crop with two upland crops (R-Mb-M) compared with intensive rice monoculture (R-R-R). This was translated in decreased bulk density and soil strength, increased soil organic carbon and total porosity, and higher aggregate stability index, plant-available water capacity, and Dexter's S index, especially at depths of 10-20 and 20-30 cm. The systems with different upland crops (maize or mung bean) showed similar high physical quality improvement. To maintain soil quality in future seasons, introducing a cropping system with at least one upland crop in rotation with rice is recommended.