Saline-alkali soil is a major constraint in agricultural production worldwide; environmentally sustainable amendment is being adopted. This study systematically investigated the effects of different concentrations of apple fermentation liquid (AFL). On rice growth under saline-alkali soil using a controlled greenhouse pot experiment. Rice plants were treated with four AFL dilutions (1:25, 1:50, 1:100 and 1:200, v/v), and the plant growth traits, development, physiological responses, biochemical characteristics, rhizosphere fungal community composition, and root transcriptome profiles were assessed. The results showed that: (1) AFL application significantly enhanced growth of rice, with the JS25 (1:25) treatment increasing plant height, stem and root length by 70.7%, 111.4% and 72.9% respectively, compared with the saline-alkali control. It also increased the antioxidant enzyme activities CAT (114.7%-232.2%) and SOD (52.5%-119.1%), and chlorophyll content (127.1%-189.6%), while indicating alleviation of saline-alkali stress by reducing proline accumulation (53.0%-74.9%); (2) High-throughput sequencing (ITS region) revealed that AFL treatment significantly altered the structure of rhizosphere fungal community, markedly increasing the relative abundance of genera such as Plectosphaerella , and Acremonium while changes in Fusarium abundance were interpreted cautiously due to its taxonomic diversity; (3) Transcriptome analysis showed that AFL treatment (JS100) induced large-scale gene expression reprograming in rice roots, including genes associated with ion transport, antioxidant defense, and stress signaling pathways. Because of the post-treatment soil physiochemical parameters and qRT-PCR validation were not conducted, the proposed mechanism should be considered exploratory and hypothesis generating. Overall, this study suggests that AFL treatment may enhance rice stress tolerance under saline-alkali conditions, as reflected in the observed physiochemical, fungal, and transcriptomic responses. However, due to the absence of post-treatment soil analysis and qRT-PCR validation, these findings should be considered exploratory and hypothesis-generating.