The soil microbial community serves as a crucial indicator for assessing soil fertility and health. The composition and activity of soil microorganisms reflect the soil's well-being and its ability to provide proper nutrients for crops. Fertilization plays a prominent role in enhancing soil fertility, and novel types of fertilizers, such as stabilized fertilizers with nitrification/urease inhibitors and coated fertilizers, have gained popularity in rice and maize cultivation. However, the long-term effects of these stabilized and coated urea fertilizers on soil chemical properties, microbial di-versity and community structure, as well as nitrogen cycling functional genes, remain unclear. Therefore, it is essential to investigate the impact of extended use of stabilized and coated urea fertilizers on soil fertility and microbiota in rice paddy fields. This research will provide scientific and theoretical support for the development and promotion of stabilized and coated urea ferti-lizers. To examine the effects of long-term application of these stabilized and coated urea fertilizers on soil chemical properties and microorganisms in rice paddy fields, soil samples were collected from brown soil rice paddy fields treated with various urease and nitrification inhibitors, stable urea, sulfur-coated urea (SCU), and resin-coated urea (PCU). The study revealed that 16 years of long-term use of conventional urea nitrogen fertilizer led to a considerable reduction in soil TP. On the other hand, NBPT and conventional urea fertilizers, when applied for an extended period, significantly increased soil organic matter (SOM). Moreover, except for HQ and NBPT+DMPP, the prolonged application of new urea fertilizers also signifi-cantly enhanced soil total potassium (TK). Notably, among all the treatments, PCU treatment had higher values for various soil chemical properties. In the case of SCU fertilizer used in brown soil rice paddy fields, it resulted in a significant decrease in soil pH over time. However, this change in pH did not affect the population of ammonia-oxidizing bacteria (AOB), as it was primarily in-fluenced by soil available nitrogen. DMPP, HQ+DCD, NBPT+DMPP, SCU, and PCU significantly reduced the copy number of bacterial 16S rRNA genes in the soil, with the coated urea fertilizers (SCU and PCU) having a greater impact. The long-term use of stabilized urea fertilizers containing HQ significantly reduced the bacterial community in rice paddy soil. Conversely, HQ+DCD stable urea fertilizer significantly increased the population structure and abundance of Basidiomycota fungi while decreasing the population structure and abundance of Rozellomycota fungi. DMPP stabilized urea fertilizer notably increased the population structure and abundance of Ascomycota fungi while decreasing the population structure and abundance of Rozellmycota and Chytridiomycota fungi. Further-more, HQ stabilized urea fertilizer significantly reduced the population structure and abundance of Chytridiomycota fungi. It is important to note that SCU fertilizer is not suitable for long-term application in neutral to slightly acidic meadow brown soil with a background pH. On the other hand, stable urea fertilizers and resin-coated urea fertilizers containing HQ, NBPT, DCD, DMPP, and their combinations are suitable for long-term application in neutral to slightly acidic meadow brown soil.