The purpose of this study is to determine ① if 3 PGPRs, (Bacillus sp. RBB1、Bacillus sp. WP8 and Pseudomonas sp. RBP1) are effective in promoting the growth of rice seedlings,②the differences between distinct applications of PGPR and the effects caused by appending fertilizer (Zhuangyangji, “ZYJ”), and ③the influences of 3 PGPRs on the structure of the indigenous bacterial community. The results were as follows: ①3 PGPRs especially for RBP1 and WP8 could promote the growth of rice seedlings, which were expressed in stocky shape and increased biomass; ②PGPR with soil drench was more efficient than seed soaking;③The effectiveness of PGPR was firstly dominated by the addition of “ZYJ”, and then by different inoculation methods; ④The above-ground dry biomass, rather than plant height, was more sensitive than other indexes, which could be used as a proper index to assess PGPR; ⑤3 PGPRs caused modest changes in the structure of the indigenous bacterial community, implied that PGPR was an eco-friendly approach to rice production. 2 PGPRs (Bacillus sp. WP8 and Pseudomonas sp. RBP1) could significantly promote the growth of rice seedlings, which implied that they have potency for microorganisms-fertilizer development.