Reclamation and restoration of saline-alkali land is of great significance for ensuring food security and protecting the red line of arable land. Planting rice and applying bio-organic fertilizer is an effective measure to remediate and improve saline-alkali land. Based on fertilizer effect of the bio-organic fertilizer, this research is conducted with measuring agronomic traits of rice at the filling stage and analyzing leaf transcriptome sequencing and the biological functions and metabolic pathways of differential genes through Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases in order to reveal the potential growth-promoting mechanism of the bio-organic fertilizer on rice grown in saline-alkaline soil. A total of four treatments were set up in the experiment, bio-organic fertilizer+chemical fertilizer (T1), bio-organic fertilizer inactivation+chemical fertilizer (T2), chemical fertilizer (T3), and blank control (T4). The results showed that the application of the bio-organic fertilizer could significantly improve rice leaf area and content of chlorophyll, number of tillers, and dry matter quantity(P<0.05); The number of differential genes of T2vsT1, T3vsT1, T4vsT1, and T4vsT3 was 6593, 4796, 6976 and 1866, respectively, and the quantity of differential gene expression was the largest for bio-organic fertilizer combined with chemical fertilizer, then for inactivated bio-organic fertilizer, the least for treatment of chemical fertilizer; GO analysis showed that the application of bio-organic fertilizer mainly influenced the biosynthesis and metabolism of rice leaf peptides and amides, translation processes, organelles and organelle membranes, etc., the differential genes were not significantly enriched (P>0.05) for biological processes of rice leaves affected by chemical fertilizers; KEGG analysis showed that the significantly different genes in the application of bio-organic fertilizer were mainly enriched in the ribosome and energy metabolism-related pathways, and ribosome-related genes expressed more differentially, perhaps there were important regulatory genes for rice to respond to the bio-organic fertilizer, the energy metabolism pathway involved photosynthesis and photosynthesis-antenna protein, the photosynthesis-antenna protein metabolism pathway-related genes were significantly up-regulated, and the number of photosynthesis and photosynthesis-antenna protein up-regulated genes in T4vsT1 greater than T3vsT1, T3vsT1 greater than T4vsT3, indicating that the application of bio-organic fertilizer could improve the light-harvesting ability of leaves and enhance photosynthesis, and the effect of bio-organic fertilizer combined with chemical fertilizer was better than that of single application of biological organic fertilizer or chemical fertilizer, T2vsT1, T3vsT1, and T4vsT1 treatment comparisons revealed that in plant hormone signal transduction the carotenoid synthesis genes were up-regulated and rice stress resistance enhanced, the number of up-regulated genes for plant-pathogen interaction metabolic pathway in T3vsT1 and T4vsT1 was more than down-regulated, indicating that the bio-organic fertilizer and bio-organic fertilizer combined with chemical fertilizer has a certain promotion effect on improving rice disease resistance. The analysis of salt-tolerant gene transcription factors showed that there were 111 transcription factors that caused rice leaves to respond to salt stress by microorganisms, 93 by bio-organic fertilizers, 97 by bio-organic fertilizers combined with chemical fertilizers, and 40 by chemical fertilizers, indicating that bio-organic fertilizer could effectively promote the expression of genes in response to salt stress in plants and enhance the salt tolerance of rice. Therefore, the application of bio-organic fertilizer in saline-alkali soil can significantly affect the up-regulation of rice ribosomal and photosynthetic genes, and the trend of up-regulation of stress resistance genes is obvious,it has a certain theoretical value for revealing the potential mechanism of rice growth promotion by bio-organic fertilizer in saline-alkali soil.