Soil aggregate fractions serve as functional units of a soil ecosystem, providing ecologically diverse microhabitats for microbial communities. Manure application has been previously reported to alter the abundance, diversity and structure of soil microbial communities. However, how manure application changes functional microbial groups and microbiome complexity in various soil aggregate fractions remains largely unclear. Here, we investigated the impact of 18-year pig manure application on microbial communities and their network complexity in soil aggregate fractions from an acidic Ultisol. Manure application significantly enhanced soil bacterial diversity rather than fungal diversity. Both manure application and aggregation had a significant impact on the bacterial and fungal community structure. Manure application reduced the relative abundance of Chloroflexi, AD3 and Basidiomycota phyla across all aggregate fractions, and enriched Proteobacteria and Ascomycota phyla in macroaggregates. As for functional microbial groups, the relative abundances of diazotrophs and bacterial nitrifiers were enhanced while bacterial denitrifiers were inhibited under manure application. Manure application increased the relative abundance of saprotrophic fungi while suppressed plant pathogens and parasites. Microbial network complexity, especially the number of positive links, increased with increasing application rates of manure. In contrast, the complexity of microbial networks declined with increasing aggregate sizes. Acidobacteria and Chloroflexi phyla comprised the majority of the potential keystone taxa in the low-rate and high-rate manure amended treatments, respectively. The importance of Chloroflexi phylum in microbial networks was promoted by manure application, despite of their reduced abundance. Together, these findings advance our understanding of the impacts of manure application on microbiome diversity, complexity and functional groups in soil aggregate fractions, with implications for managing agricultural ecosystem functioning in Ultisols.