<p>This study aimed to elucidate the effects of saline-fresh water rotational irrigation on the root microenvironment of tomatoes, which is crucial for optimizing the saline water irrigation strategies. A two-season tomato experiment was conducted in a greenhouse in southern Xinjiang, with three saline-fresh water rotational irrigation treatments (W1, W2, W3) and a freshwater control (CK). The main focus was on the effects of saline-fresh water rotation irrigation on the physicochemical properties, enzyme activity, and microbial community structure of the tomato rhizosphere soil. The implementation of saline-fresh water rotational irrigation strategies was an effective means of maintaining the abundance and diversity of beneficial microorganisms in the tomato rhizosphere soil, positively impacting soil nutrient availability and enzyme activity. Soil enzyme activity and nutrient content showed a significant increase in the W1 and W3 treatments compared to the control treatment. The W3 treatment significantly improved the soil microenvironment and conserved freshwater, while ensuring no significant yield reduction compared with the CK treatment. The relative abundance of <i>Actinobacteriota</i> was reduced t<i>o</i> varying degrees in different saline-fresh water rotation irrigation treatments, while that of beneficial microorganisms such as <i>Firmicutes</i>, <i>Bacteroidetes</i>, <i>Verrucomicrobiota</i>, and <i>Bacillus</i> increased. In autumn, cold-loving bacteria such as <i>Paenisporosarcina were prominent</i>. These beneficial microorganisms enhance tomatoes’ ability to resist saline-alkali stress. The W3 treatment demonstrated a stronger ability to recruit beneficial microorganisms, likely due to host specificity and higher productivity. Therefore, the W3 treatment is recommended as an effective saline water application method for improving the root microenvironment of greenhouse tomatoes.</p>