Rising freshwater scarcities pose a serious threat to agricultural production. Reclaimed water (RW) is increasingly utilized as one of the alternative resources for irrigation in agriculture. Microbial communities play crucial roles in the soil microenvironment and can be used as effective indicators to assess the ecological influence of RW irrigation in soil. However, there is a lack of research on the effects of RW with different irrigation techniques on soil attributes and microbial communities. The present experiment was conducted in China to investigate the effect of two kinds of water qualities (RW and clean water (CW)), two kinds of irrigation methods (full irrigation (FI) and alternate partial root-zone irrigation (APRI)), and two kinds of irrigation techniques (furrow irrigation (FUI) and subsurface drip irrigation (SDI)) on soil chemical properties, heavy metal concentrations, and bacterial community structure. The APRI treatments received 70% of the irrigation water volume of FI. The results revealed that electrical conductivity (EC), nitrate nitrogen (NO3−-N), and heavy metal (Cu, Cd, Pb, Zn) concentrations in soil irrigated with RW were significantly higher in comparison to the soil irrigated with CW. SDI significantly decreased the contents of TN by 4.88%, the EC by 13.78%, and the heavy metal Cd concentration by 13.14% in soils than that irrigated with FUI treatment. APRI significantly decreased the heavy metal Cu concentration in soils by 6.26% compared to FI treatment. Proteobacteria, Chloroflexi, Acidobacteria, and Gemmatimonadetes in soil irrigated with RW were more abundant than that irrigated with CW. The irrigation water quality, soil moisture content, heavy metal content, TN, and EC under various irrigation techniques and methods significantly affected the structure of soil bacterial communities. In conclusion, we highlight that the SDI-APRI treatment can be an efficient irrigation practice for reducing the EC, heavy metal pollution, and the security risks of soil irrigated by RW.