Biological nitrogen fixation is the major source of nitrogen in Pinus massoniana areas, and the nitrogen supply and soil fertility maintenance can be largely affected by the composition and quantity of the nitrogen-fixing bacterial community. In this study, pool cultivation experiments were conducted to analyze the relationship between the soil chemical behavior and structure and abundance of the nitrogen-fixing bacterial community in Pinus massoniana soil developed from different parent rocks (blastopsammite, quartzose sandstone, feldspathic quartz sandstone, and basalt). The fluorogenic quantitative real-time PCR technique was adopted in the experiments using the high-throughput sequencing platform Illumina Miseq to target the nifH gene. The results showed that: (1) the Basalt had higher amounts of organic carbon, total nitrogen, alkaline nitrogen, and microbial biomass nitrogen with larger plant height and diameter compared with other types of parent rocks(P < 0.05). (2) The abundances of the nifH gene varied significantly for the four types of parent rocks; more specifically, the nifH gene abundances of basalt were 3.75, 7.89, and 4.41 times higher than those of blastopsammite, quartzose sandstone, and feldspathic quartz sandstone, respectively. (3) The diversity index α (abundance and diversity) of the four types of parent rocks was significantly different, and basalt showed a considerably higher α than that of other parent rocks. In total, 159,231 valid sequences, which belong to 6 phyla, 14 classes, 69 orders, and 122 genera, were obtained from the soil of the four parent rocks. Proteobacteria and Cyanobacteria were the dominant phyla, whereas Bradyrhizobium, Calothrix, Rhizobium, and Azospirillum were the dominant genera. Compared with other parent rocks, basalt had higher abundances of Proteobacteria, Calothrix, Rhizobium, and Azospirillum. The results from hierarchical clustering and non-metric multidimensional scaling (NMDS) showed that for the nitrogen-fixing bacterial community, quartzose sandstone and feldspathic quartz sandstone shared a similar structure, whereas basalt had a different structure compared with the other types of parent rocks. (4) The amounts of organic carbon, total nitrogen, alkaline nitrogen, and microbial biomass nitrogen were the main factors for the abundance of nitrogen-fixing bacteria, the diversity of α, and the structure of the bacterial community. In general, basalt soil had a high fertility, increased the amount of nitrogen-fixing bacteria, and enhanced the diversity of the bacterial community, thereby facilitating the growth of Pinus massoniana. Our study provides a scientific basis for selecting the appropriate growth environment and nitrogen adjustment for Pinus massoniana from a microbiological point of view.