[Objective] Loess-paleosol sequence (LPS) is a good carrier recording the changes of Quaternary climate and environment, and the characteristics of soil microorganisms in it indicates important information about the changes of soil environment. Due to the climate difference between loess and paleosoil, the soil microbial community may have different responses in the structural characteristics. The research on this problem, however, is limited. [Methods] In this paper, the loess (RL and JL)-paleosol (RS and JS) sequences in Renjiapo (R) and Jiuzhoutai (J) were selected, and high-throughput sequencing and linear discriminant analysis effect size (LEfSe) were employed to gain insights into the community structure and group differences of soil prokaryotes. Furthermore, functional annotation of prokaryotic taxa (FAPROTAX) was used to predict the community function, and the Mantel test was carried out to identify the environmental factors affecting the community stability of soil prokaryotes. [Results] The carbon and nitrogen in soil showed changes consistent with the magnetic susceptibility and Rb/Sr ratio, the alternative indicators of climate change. The content of carbon and nitrogen was high in the paleosol (RS and JS, especially in RS) and low in the corresponding loess (RL and JL). In the same climate era, Jiuzhoutai was drier and colder than Renjiapo. The paleosol deposition stage in Jiuzhoutai was affected by strong winter monsoon, which ultimately led to the gradual change from the dry-cold to wet-warm climate. In the prokaryotic community, thermophilic or mesophilic bacteria and archaea, such asAcidobacteria,Crenarchaeota, andChloroflexi, were abundant in RL and RS, while those with tolerance to drought and extreme environments, such asGemmatimonadetes,Actinobacteria,Firmicutes,Euryarchaeota, andDeinococcus-Thermus, had high abundance in JL and JS. The functional genes related to energy source and nitrogen, manganese, iron, and chlorine cycling had the highest expression levels in RS, while those involved in carbon, hydrogen, and sulfur cycling showed the highest expression levels in RL. The prokaryotic community in Jiuzhoutai had higher species diversity and fewer functional species than that in Renjiapo. Mantel test results indicated that soil organic carbon (SOC), soil water content (SWC), total nitrogen (TN), and nitrate nitrogen (NO₃⁻-N) were the key environmental factors influencing the stability and functions of the prokaryotic community in Renjiapo, while the influencing factors in Jiuzhoutai were TN, SOC, pH, and ammonium nitrogen (NH₄⁺-N). [Conclusion] During the warm-humid period, the microbial community differentiated into more functional categories and exhibited more vigorous life activities. When the climate was dry and cold, the microbial community completed the main life activities by improving species diversity and jointly maintaining the community survival and stability to adapt to environmental stress. The findings are of great significance for understanding the impacts of climate change on the diversity and functions of soil microorganisms.