Transformation of organic amendments in soil greatly affects its physical, chemical, and biological properties. The aim of this study was to investigate changes of soil quality attributes in field plots after 3-5 years of annual paddy-upland crop rotation with various fertilizations since 1995. Other than the amendments of green manure, compost, and peat, chemical fertilizer N in the amounts of 33% and 67% of established N rate were complemented. Spring rice (Oryza sativa L.) and autumn maize (Zea mays L.) were planted each year. After the harvests of three to five maize and rice crops from 1998 through 2000, surface soil samples were collected from the plots of each treatment. Applications of organic materials to the plots prevented soil pH from decreasing, and increased the amounts of soluble salts. After rice harvest, the soil water contents at 0.033 MPa tension were significantly greater in soils amended with peat and/or compost than that with chemical fertilizer and the check. The bulk density of surface soils of the field plots amended with organic materials was significantly lower than that of the check. After maize harvest, the differences in bulk density of the surface soils among the seven treatments were not significant. The percentages of water stable aggregate in 1-2 and 0.5-1 mm particle size fractions of the soils, amended with peat and compost, were significantly higher than those amended with chemical fertilizer and the check. Although chemical fertilizer played a significant role in governing the maize and rice yields, it did not significantly contribute to the improvement of some soil quality attributes.