Our aim was to investigate the impacts of different raw materials on the microbial diversity in traditional fermented sour porridge and the physiological characteristics of strains isolated from it. Five lactic acid bacterial (LAB) strains (SXZ 6, SZ 2, SZ 4, SMF 3 and SXZ 7) and three yeast strains (SXZ 9, SZ 1+ and SMF 5) were isolated by conventional methods from three fermented sour porridges collected from Qingshuihe County, Inner Mongolia for analysis by high-throughput sequencing. The results indicated that the predominant bacterial genera were Lactobacillus, Acetobacter and Lentilactobacillus, and the dominant fungal genera were Issatchenkia, Alternaria and Pichia. Physiological characterization revealed that after 48 h incubation, all LAB strains reduced the pH to 3.66–3.70. Strain SMF 5 exhibited outstanding gas production performance, SXZ 6 and SZ 1+ exhibited good acid tolerance, and SZ 4 and SMF 5 showed good bile salt tolerance. Additionally, strains SXZ 7 and SXZ 9 scavenged 91.78% and 93.6% of 1,1-diphenyl-2-picrylhydrazyl radical, respectively, while no significant difference was observed in their superoxide anion scavenging capacity. Overall, these results indicated that different raw materials significantly influenced the microbial community structure and functionality in sour porridge, with different cereal combinations specifically promoting bacterial or fungal aggregation. All isolates had good physiological properties, showing great potential for application in food fermentation.