The majority of marine ammonia oxidizers belong toThaumarchaeota, a phylum of Archaea, which is distributed throughout the water column. Marine surface waters contain distinct thaumarchaeotal phylotypes compared to the deeper ocean, but spatial dynamics of the surface-associated lineages are largely unsolved. This study of 120 seawater samples from the eastern Chinese marginal seas identified contrasting distribution and association patterns among thaumarchaeotal phylotypes across different dimensions. Horizontally,Nitrosopumilus-like andNitrosopelagicus-like phylotypes dominated the surface water (3 m) of the Yellow Sea (YS) and East China Sea (ECS), respectively, along with increased abundance of total free-livingThaumarchaeotain ECS. Similar compositional changes were observed in the surface microlayer. The spatial heterogeneity of particle-attachedThaumarchaeotawas less clear in surface microlayers than in surface waters. Vertically, theNitrosopelagicus-like phylotype increased in abundance from surface to 90 m in ECS, which led to an increase in the proportion ofThaumarchaeotarelative to total prokaryotes. This occurred mainly in the free-living fraction. These results indicate a clear size-fractionated niche partitioning, which is more pronounced at lower depths than in the surface water/surface microlayer. In addition, associations ofThaumarchaeotawith other microbial taxa varied between phylotypes and size fractions. Our results show that a phylotype-resolved and size-fractionated spatial heterogeneity of the thaumarchaeotal community is present in surface oceanic waters and a vertical variation of theNitrosopelagicus-like phylotype is present in shallow shelf waters.Supplementary InformationThe online version contains supplementary material available at 10.1007/s42995-023-00169-y.