Understanding microbial community succession is key to uncover the mechanisms driving variation in soil fertility under rice cultivation. To evaluate microbial community divergence along paddy soils after 9, 15 and 25 years of cultivation with and without intensive fertilization, 16S rRNA gene high throughput sequencing and network co-occurrence analysis were used. Except for the initial barren soil, three different fertilization treatments were applied to rice planted soil: control (CK, without fertilization), NPK (N + P + K), and NPKM (NPK plus manure). Fertilization increased the difference of microbial species abundance between rice paddy soil and the initial barren soil reflecting higher C input by roots under fertilization. The bacterial communities after 9 and 15 years of rice cultivation clustered together and differed from those in barren soil and after 25 years of rice cultivation. Oligotrophic bacterial groups in the fertilized soil were gradually substituted with copiotrophic microorganisms during rice cultivation. The redundancy analysis indicated that the divergence in the microbial community structure during rice cultivation increased with soil organic C and total N. The network co-occurrence analysis showed that microbial network in NPKM soil contained the largest ratio of positive to negative links, whereas the CK network contained the smallest. Hence, fertilization and its duration control the distribution of keystone species and the nature of the links established between them. © 2019 Elsevier B.V.