【Objective】The high-throughput sequencing technology can easily access the species varieties and the relative abundance of a microbial community. Nevertheless, the relative abundance cannot fully reflect the microbial quantities when using it to evaluate the community. On the other hand, the absolute abundance which is one of the essential parameters for describing a microbial community structure in ecology has been ignored. The absolute abundance can be calculated by integrated high-throughput absolute abundance quantification (iHAAQ); which combines high-throughput sequencing and quantitative PCR (qPCR). Both relative and absolute abundances are essential parameters for describing a microbial community structure in ecology. The relative abundance could describe and evaluate the relationship of specific taxa with others in the same sample, while the absolute abundance as a constant parameter is more suitable for describing and evaluating the quantitative variations of specific taxa in a sample or among samples. Thus, this study aimed to provide a comprehensive and in-depth analysis of soil microbial community through the relative and absolute abundances of the archaeal, bacterial, and eukaryotic (fungi) domains of microorganisms (described as three-domain microorganisms).【Method】Based on data of soil microbial community in the studies of banana panama disease, the reclaimed sandy agricultural ecosystem and microbial inhibitor, the absolute abundances of archaea, bacteria and fungi in three papers were obtained by iHAAQ. Then the absolute and relative abundances of three-domain microorganisms were further calculated. The α- and β-diversity analyses of archaea, bacteria, fungi and three-domain microorganisms were conducted according to their relative and absolute abundances, respectively.【Result】The results showed that: (1) Compared to archaea and fungi, the bacteria dominated the soil microbial community with higher species varieties and absolute abundance. Meanwhile, the lack of absolute abundance parameters might lead to the misunderstanding of the microbial community. (2) The α-diversity indexes calculated by relative and absolute abundances were the same, while the β diversity indexes were different. (3) In the research of banana panama disease and reclaimed sandy agricultural ecosystem, PCoA results of three-domain microorganisms and bacteria were relatively similar, which indicated that the community structures of three-domain microorganisms were mainly affected by bacteria in these two studies. But no similar results were found in the research of microbial inhibitors.【Conclusion】The iHAAQ method can be applied to the studies that perform high-throughput sequencing and qPCR analyses, simultaneously. It is of great ecological significance to study the three-domain microbial community with the species varieties, relative and absolute abundances obtained by the iHAAQ method, and it should be encouraged for future research.