Rhizosphere microbiota are conducive to soil nutrient cycling for plant growth. Long-term and excessive application of chemical fertilizer is harmful to agriculture. Seaweed extract is a good organic substitute for rhizosphere ecosystem and plant growth. We supplemented 5‰ seaweed extract powder to chemical fertilizer, and then studied its effect on rhizosphere bacteria of japonica rice (Oryza sativa L. subsp. japonica). In a short-term experiment, we compared the changes in rhizosphere bacteria among four treatments, i.e., no fertilizer (T1), chemical fertilizer only (T2), chemical fertilizer with 5‰ seaweed extract (T3), and less chemical fertilizer with 5‰ seaweed extract (80% of that of T3) (T4). Results show that seaweed extract supplement could affect the bacterial community in tillering and heading stages; the α-diversity of rhizosphere bacteria in the heading stage was obviously improved. In addition, seaweed extract supplement improved significantly the content of nitrate nitrogen (N), available phosphorus (P), and available potassium (K) in rhizosphere soil in the tillering stage, and, finally, increased the rice yield and quality mildly. Therefore, the seaweed extract supplement is shown to be a potential strategy to enrich the diversity of rhizosphere bacteria, which enhanced soil nutrient level, increased rice yield and quality, and also saved the use of chemical fertilizer.