Efficient saline-water use in arid greenhouse production requires irrigation schedules that coordinate salt exposure with crop salt-sensitivity windows while limiting residual soil salinity. This three-season greenhouse experiment in southern Xinjiang evaluated how the timing of saline-water application under saline-freshwater rotation affected root-zone water-salt dynamics, tomato growth kinetics, and yield formation. Tomato cultivar ‘Mingzhu’ was grown under a freshwater control (CK) and three rotation schedules with the same irrigation amount and saline-water input: After two initial freshwater irrigations common to all treatments, the eight rotation events were W1, S-F-S-F-S-F-S-F; W2, S-S-F-F-S-S-F-F; and W3, F-F-S-S-S-S-F-F, where S and F denote saline-water and freshwater irrigation, respectively. Mean 0–80 cm root-zone water content and salinity, plant height, leaf area index, aboveground dry matter, and yield were monitored, and Logistic growth analysis and partial least squares path modeling were used to identify the water-salt-growth-yield pathway. In the rotation treatments, root-zone salinity varied with saline-water timing. W1 and W2 accumulated salts earlier, whereas W3 delayed the major salt-accumulation pulse until fruit enlargement, when its salinity increased rapidly and exceeded that under W1 and W2 before declining after final freshwater irrigation. Thus, W3 redistributed salt stress over time rather than continuously maintaining the lowest salinity. These results suggest that saline-freshwater rotation should be designed according to crop salt-sensitivity windows and late-season leaching requirements. Under the tested sandy-loam greenhouse conditions, the W3(F-F-S-S-S-S-F-F) schedule is a conditionally promising strategy for balancing saline-water use and tomato yield stability in southern Xinjiang.