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The application of organic fertilizers affects soil aggregates, nutrient situations and bacterial communities. However, the direct and indirect effect of different resource-derived organic fertilizers on soil bacterial communities and their links to soil aggregate is poorly understood. Here, we carried out a field experiment for three years to investigate the linkages between soil aggregates and bacterial diversity in a dryland red soil. Six treatments were compared: (no fertilizer (CK), chemical fertilizer (CF), 60% chemical fertilizer + straw at 4500 kg ha−1 (RFS), 60% CF + biochar at 1500 kg ha−1 (RFB), 60% CF + pig manure at 15000 kg ha−1 (RFP), and 60% CF + vermicompost at 15000 kg ha−1 (RFV)). The application of pig manure or vermicompost (animal-derived organic fertilizer) enhanced the soil pH, the content of large macroaggregate (>2 mm), organic matter, available phosphorous and available nitrogen, while decreased the content of small macroaggregate (0.25–2 mm) and microaggregate (<0.25 mm) compared with other treatment. Relative abundances of the dominant bacterial phyla varied across chemical and organic fertilizer treatments, primarily by increasing Bacteroidetes, Gemmatimonadetes, and decreasing Chloroflexi, Acidobacteria and Planctomycetes. Organic fertilizers particularly animal-derived organic fertilizer enhanced the Richness, Shannon and Pielou indices of soil bacteria compared with chemical fertilizer treatment. The regulation of animal-derived organic fertilizers on bacterial community structure (accounting for 53.04% of the variance) was greater than that of plant-derived organic fertilizers (straw and biochar, accounting for 7.69% of the variance). The bacterial alpha diversity showed positive correlation with large macroaggregate, but a negative correlation with small macroaggregate. Further, structural equation models indicated that animal-derived organic fertilizers impacted bacterial diversity positively by regulating resource availability through soil aggregates. However, for the plant-derived organic fertilizers, bacterial diversity was negatively affected by soil aggregates alone, but this was not regulated by fertilization. In addition, animal-derived organic fertilizer also positively affected soil bacteria diversity indirectly via changing soil pH and resource availability. Overall, the different impacts of animal- and plant-derived organic fertilizers on soil bacterial community highlighting the pivotal role of soil habitat architecture and resource chemistry changed by organic fertilizers in the regulation of soil bacteria, which may influence soil quality and agricultural sustainable development. • Animal-derived organic fertilizer (AOF) decreased 0.25–2 and <0.25 mm soil aggregates. • AOF increased >2 mm soil aggregates, pH, organic matter, available P and N. • AOF affect soil bacterial community structure than plant-derived (POF). • AOF affect bacterial community mainly via changing aggregates, pH and resource availability. • Aggregates affect bacterial diversity alone under POF, but not regulated by fertilization. [ABSTRACT FROM AUTHOR]