Incorporation of crop residues into agricultural soils is a common practice that can improve soil quality. However, the impact of different straw incorporation techniques on soil bacteria and their functions is still not well understood, especially across soil depths. Here, we investigated the impact of three maize straw management methods (straw removal, straw incorporation into topsoil, and deep‐injected straw incorporation into subsoil) on soil bacterial communities and how they were linked to extracellular enzymes and soil properties. Deep‐injected straw incorporation strongly promoted enzyme activities: C‐cycling enzymes increased by 111–532 nmol g−1 hr−1, N‐cycling enzymes by 229–708 nmol g−1 hr−1, and P‐cycling enzymes by 142–216 nmol g−1 hr−1 compared to straw removal and straw incorporation into topsoil. In addition, deep‐injected straw incorporation considerably increased soil organic carbon (SOC), dissolved organic carbon (DOC), and total nitrogen (TN) compared to the other straw management methods (249–253% for SOC, 303–370% for DOC, and 178–196% for TN). However, in topsoil, only minimal effects of straw management practices on bacterial communities, enzymes activities, and soil properties were found. Deep‐injected straw incorporation favoured copiotrophic bacteria which resulted in a reduction of 41% in Shannon index. Bacteria associated with carbon and nitrogen cycling were mainly Actinobacteria, which were positively correlated with TN, SOC, and DOC. Acidobacteria were the dominant species in P‐cycling module and were positively associated with SOC, DOC, and available phosphorus. Overall, injection of straw into subsoil alters bacterial communities and functioning, and increases soil nutrients and soil organic C in subsoil.