China has widely implemented land consolidation, which was expected to increase the amount of cultivated land and enhance grain yields. Key components of land consolidation include filling mall waterbodies and leveling land, both of which have strong impacts on the environment in the Yangtze River Delta. The impacts of land consolidation on soil ecology and agricultural production are not yet clear. Here, we conducted a field survey of soil properties and rice growth to detect the effects of land consolidation in the first growing season. The normalized difference vegetation index (NDVI) was used to analyze the remote sensing data. We found significant differences in the soil properties under different types of land leveling, with a general NDVI pattern of: control > borrowed topsoil area > filled waterbodies area > topsoil cutting area. We found significant heterogeneity in rice NDVI after land consolidation. The NDVI of rice had extremely significant positive correlations with soil organic matter and available zinc. The spatial variation in soil properties caused by land consolidation was a dominant factor leading to the heterogeneity of rice NDVI. Fertilizing soil and strengthening field management should be adopted to provide more ecological services while increasing quantity.