Intensified livestock system produced large amount of bio-waste, and improper disposal of livestock manure has led to severe environmental consequences. However, knowledge about the time-dependent changes of manure-derived nitrate and soil bacterial diversity along the soil profiles is limited. In this study, vertical variation of soil bacterial diversity and composition in a manure-amended maize field and adjacent non-manured woodland was investigated using high-throughput sequencing technique in spring and autumn along a 1-meter profile depth. The results showed that higher amount of nitrate was detected along the soil profile loaded with cattle manure compared with the adjacent non-manured woodland, and soil δ15N-NO3- composition further corroborated the manure-derived nitrate in the maize field. No significant difference in bacterial richness between the two land uses was found, while clear separation of bacterial structure was detected even to the deep soil layers. Canonical correspondence analysis showed that soil properties were the major factors influencing the variance of bacterial community composition. Bacterial network is more complex in the maize field than in the adjacent woodland. Soil bacterial communities among the depth profiles in the two land uses tended to be more phylogenetically clustered than expected by chance, and were more likely to be clustered along the depth. These findings suggested that bacterial β diversity was strongly related to multi-nutrient properties with high livestock manure load, and had important implications for assessing the environmental impacts on below-ground biodiversity in sandy loam soils.