BackgroundUnderstanding the enhancement of salt tolerance and crop growth in agricultural system through magnetized‐ionized water irrigation is crucial for advancing agricultural practices.MethodThis study examined the impacts of fresh water (F), brackish water (B), magnetized‐ionized fresh water (MIF), and magnetized‐ionized brackish water (MIB) on soil properties and the growth of cotton seedlings through microbial analysis during the cotton seedling period.ResultsThe results revealed that magnetized‐ionized water irrigation improves soil water retention and promotes salt leaching. In comparison to F irrigation, plant height, leaf area index (LAI), dry matter accumulation (DM), chlorophyll content (SPAD) levels increased by 3.61%, 4.07%, 5.76%, and 1.33%, respectively, under MIF irrigation. Similarly, when compared to B irrigation, LAI, DM, and SPAD increased by 5.13%, 6.12%, and 3.12% under MIB irrigation. Furthermore, magnetized‐ionized water irrigation led to a notable rise in the relative abundance of beneficial soil bacterial communities, particularly Pseudomonas and Azoarcus, as well as fungal like Trichoderma, while decreasing the prevalence of pathogenic fungi, such as Lasionectria, Gibberella, and Alternaria. Notably, this irrigation approach induced alterations in soil properties, and the partial least squares path modeling revealed significant links between soil properties and both cotton growth and fungal community structure (with path coefficients of −0.884 and 0.693, respectively).ConclusionThis study elucidated the distinct impacts of soil properties and growth indices on cotton yield during the seedling period, providing a crucial scientific foundation for enhancing future agricultural production through the use of magnetized‐ionized water irrigation.This article is protected by copyright. All rights reserved.