Coastal marshes are transitional areas between terrestrial and aquatic ecosystems and vulnerable to climate change and anthropogenic activities. In recent decades the reclamation of coastal marshes remarkably increased and their effects on microbial communities present in coastal marshes have been studied with great interest. However, most of these studies focused on microbial community composition and diversity. The processes underlying functional community assembly and spatiotemporal effect often ignored. Therefore, community structure and assembly mechanisms of ammonia-oxidising prokaryotes in long-term reclaimed coastal marshes have not been studied. Here using qPCR and IonS5TMXL sequencing platform, we investigated spatiotemporal dynamics, assembly processes and diversity patterns in ammonia-oxidising prokaryotes in over 1000 years reclaimed coastal salt marsh soils. The taxonomic & phylogenetic diversity and composition of the ammonia-oxidizers showed apparent spatiotemporal variations along reclamation of soil. The phylogenetic null modelling-based analysis showed across all sites, the archaeal ammonia-oxidising community assembled by deterministic process (84.71%). The ammonia-oxidising bacterial community was formed more by a stochastic process in coastal marshes and at stage 60 years (|βNTI|<2), despite its relatively dominant deterministic process (55.2%). The deterministic assembly process and nitrification activity in reclaimed soils was positively correlated. Archaeal amoA gene abundance were also positively correlated with the nitrification rate. Our study revealed that during the 1000 years of reclamation coastal marshes both ammonia-oxidising communities responded differently to diversity change and assembly processes and nitrification activity. These findings provide a better understanding of how long-term reclamation affect soil N cycling and assembly dynamics of ammonia-oxidising communities.