This study aimed to evaluate the effects of biochar application on soil physicochemical properties and aggregate structure of saline soil under different water supply scenarios, with dry–wet alternation frequency serving as a key indicator of water regime variability. [Methods] A soil column incubation experiment was conducted with four biochar treatments: no biochar (CK), low (SWL), medium (SWM), and high (SWH) application rates. Three dry–wet alternation frequencies (DRW2, DRW4, and DRW6) were established to simulate typical water supply conditions under low, moderate, and high rainfall or irrigation intensities, respectively. [Results]①Dry–wet alternation frequency significantly influenced soil salinity and bulk density, both of which showed an overall increasing trend with increasing alternation frequency.②Across all water regimes, biochar application significantly reduced soil salinity and bulk density, alleviating soil compaction.③Biochar also promoted the formation of macro-aggregates and large micro-aggregates, leading to a marked improvement in aggregate stability.④The enhancement of aggregate stability depended on both biochar application rate and water regime. The low biochar rate (SWL) was more effective under low-frequency dry–wet alternation (DRW2), whereas the medium rate (SWM) better maintained aggregate stability under moderate and high alternation frequencies (DRW4 and DRW6).⑤Correlation and principal component analyses showed that aggregate stability was positively associated with soil organic matter, polysaccharides, amorphous iron oxides, and iron oxide activation degree, while soil salinity was negatively correlated with these binding agents. [Conclusion] Biochar application consistently improved saline soil structure under different water supply scenarios, with its regulatory effects on aggregate stability strongly dependent on dry–wet alternation frequency.