It is to screen microaerobic Fe2+ ^{oxidizing bacteria (FeOB}) with better oxidative abilities to Fe2+ ^{and to evaluate} its effects on improvement of gleyed paddy soils and soil microbial communities and functions, laying a foundation for establishing microbial improvement technologies of gleyed paddy fields. FeOB were enriched using Modified wolf’s mineral medium. The FeOB strain was taxonomically identified by combined technologies, including 16S rRNA sequencing, et al. Pot experiments were conducted to evaluate the effects of the strain on soil reducing substances, soil nutrients, nitrogen cycling functional gene (NCFG) abundances and rice seedlings in gleyed paddy soils. The impacts on the soil micro-ecology were examined using 16S rRNA high-throughput sequencing technology. As a result, a FeOB strain exhibiting a strong oxidative effect on Fe²⁺ was obtained and was subsequently identified as Lysinibacillus sphaericus WH07. The 100 mL fermentation liquids of the strain WH07 were used to treat gleyed paddy soil with different concentration of 106 ^(T1), 107 ^(T2), 108 (T3) CFU/mL, respectively. Compared to the control, the soil redox potentials (Eh) were significantly increased (P<0.05), being changed from negative to positive potentials. The total reducing substances, the ferrous contents, and the manganese contents, all were decreased by 0.37%?53.19% in all three treatments and were significantly decreased in both T2 and T3 (P<0.05). Five routine indicators of the soils, including the alkaline hydrolyzed nitrogen contents, et al., were all significantly increased by 3.40%?49.90% (P<0.05). Four NCFG, including AOA-amoA, et al., were increased or significantly increased in abundance compared with the control. The physiological indicators of rice seedlings, including plant heights, et al., were higher or significantly higher than the control. Both Chao1 and Shannon α diversity indexes were significantly decreased than the control (P<0.05). Among top 10 phyla of soil bacteria, 8 phyla were significantly down-regulated, including Proteobacteria, et al., while 2 phyla (Bacteroidetes and Firmicutes) were significantly up-regulated. Among top 50 genera, a total of 20, 19, and 22 genera were significantly up-regulated respectively in three treatments (P<0.05), including 6 FeOB, such as Macellibacteroides, et al., while 25 genera were significantly down-regulated in all three treatments (P<0.05), composing of 4 Fe reducing bacteria, such as MBNT15, et al. Analysis of the regulating network showed that the strain WH07 potentially coordinated with other FeOB improved soil physiochemical properties and biological activities, finally improving the growth of rice seedlings. The results of this study showed that application of the strain WH07 significantly improved the physiochemical properties of the gleyed rice soil and significantly changed soil microbial communities and functions, laying a foundation for research and development of highly efficient microbial agents improving gleyed paddy soils.