Hongjiannao Lake, once the largest desert freshwater lake in the arid and semi-arid regions of China, has undergone progressive salinization and ecological degradation over recent decades. During salinization, the cascade effect formed by the molecular transformation of dissolved organic matter (DOM) and the succession of microbial communities has emerged as a key mechanism for unraveling the internal processes of ecosystem degradation. In this study, we integrated hydrochemical parameters, DOM properties, and high-throughput sequencing of 16S rRNA genes to investigate microbiota differentiation and its environmental drivers along the river-lake continuum of the Hongjiannao watershed. The results showed that salinization drove molecular reconstruction of DOM, with a 37.6% decrease in humic-like components and an 84.7% increase in protein-like components. Increases in spectral slope ratio (SR) and specific UV absorbance at 254 nm (SUVA254) further indicated the breakdown of terrestrial humic substances into smaller aromatic molecules. Concurrently, the microbial community exhibited significantly suppressed alpha diversity and reduced spatial heterogeneity; the abundance of ubiquitous freshwater taxa declined, whereas salt-tolerant bacteria (e.g., certain members of Actinomycetota and Cyanobacteriota) increased. Furthermore, the number of functional annotation categories decreased, and the complexity and stability of the microbial co-occurrence network dropped sharply. Salinization drives microbial community reassembly through both direct pathways and indirect effects mediated by DOM transformation. This study reveals a cascading mechanism whereby salinization stress alters DOM bioavailability, leading to a loss of microbial diversity and functional narrowing, ultimately degrading lake ecological functions. We propose an integrated restoration strategy, including ecological water replenishment, introduction of salt-tolerant microbial consortia, and regulation of DOM inputs. This study provides a systematic, microbiome-based framework for the ecological management and restoration of salinized lakes in arid regions.