Soil and rhizosphere microorganisms play essential roles in nutrient cycling and plant growth promotion in agricultural systems. Natural mineral materials, such as zeolite, are widely used as soil amendment materials to create “healthy” conditions for microorganisms related to plant cultivation. However, the effects of these minerals on microbial community structures in the soil with different aggregate scales and rhizosphere are largely unknown. In this study, we used cherry tomato (Solanum lycopersicum L. var. cerasiforme) cultivation experiment fed with 80 kg/1000 m2 green tuff (GT) as a natural soil amendment material and without GT (control blank as conventional farming; CK). The total yield and average root weight in GT were 1.2-fold and 1.6-fold higher than those in CK, respectively. The 16S rRNA gene amplicon sequence analysis in size-fractionated soil samples showed that the genus Bacillus, known as plant growth-promoting bacteria (PGPB), was significantly increased in bulk soil (nonfractionated soil), large macroaggregates (LMA, 5.6 mm–1 mm diameter), and small macroaggregates (SMA, 1 mm–250 μm diameter) in GT, and the genus Nocardioides, known as PGPB, was significantly increased in the rhizosphere of GT compared with CK (p < 0.05). These microorganisms had significant positive correlations with several PGPB, such as Bacillus, Nocardioidaceae, and Mesorhizobium. These results suggest that green tuff supplementation improves the microbial interactions in the soils, yields and root weight of cherry tomato.