Abstract: The comprehensive effects of different algal oligosaccharide bio-fertilizer treatments on the yield, relative chlorophyll content, grain properties, root soil physical and chemical properties and microbial community of Yongyou 1540 rice were studied. Four treatment were set up:Treatment A, 66.7% algal oligosaccharide with 33.3% Bacillus mucilaginosus; Treatment B, 100% algal oligosaccharide; Treatment C, 100% Bacillus mucilaginosus; CK, 100% clean water. A total of 1 basal fertilizer and 3 foliar spraying were applied. The results showed that the hybrid rice leaf in treatment B had the highest relative chlorophyll content. The increased production in treatment A was the most significant, reaching 13.2%, while that of treatment B and C was 5.6% and 10.9%, respectively. The content of N, P and K in rice grains with the increased application of algal oligosaccharide was generally higher than that of the control. Meanwhile, pH value of root soil in treatment B was the highest, while the relative content of Acidobacteria was the lowest, showing a significant negative correlation. Both algal oligosaccharide and Bacillus mucilaginosus could promote the yield of Yongyou 1540, but the synergistic effect was obvious after the combination.