To obtain protease- and lipase-producing halotolerant/halophilic strains suitable for shrimp paste (SP) fermentation, the microbial community structure and enzyme-producing microbial species were analyzed and predicted using metagenomics in 3 high-salt samples. Based on the linear salt gradient method, 128 strains were screened. Eight halotolerant/halophilic strains highly producing 2 types of enzymes were identified and inoculated into low-salt SP to assess the heterogeneity of SP. Physicochemical properties of SP indicated that Bacillus subtilis XJ-11, Virgibacillus halodenitrificans XJ-229, Piscibacillus halophilus XY-193, and Bacillus vallismortis HT-73 were more suitable for rapid fermentation of SP. Nutritional analysis showed that SP inoculated with V. halodenitrificans XJ-229 had the highest free amino acid content and SP inoculated with P. halophilus XY-193 had the highest unsaturated fatty acid content. The former had prominent umami, sweetness, and meaty aroma, weak bitterness and fishy flavor, and the closest flavor to the control (CP) based on sensory evaluation and E-nose analysis. A total of 61 volatile compounds were detected in all samples by SPME-GC-MS, of which 32, 23, 40, 24, and 28 were detected in the CP and SP inoculated with B. subtilis XJ-11, V. halodenitrificans XJ-229, P. halophilus XY-193, and B. vallismortis HT-73, respectively, with 12, 11, 12, 9, and 9 key flavor compounds. Among several samples, the highest levels of pyrazines, aldehydes, alcohols, and ketones were found in SP inoculated with B. subtilis XJ-11, V. halodenitrificans XJ-229, P. halophilus XY-193, and B. vallismortis HT-73, respectively. These results suggested that inoculation of different enzyme-producing halotolerant/halophilic strains resulted in differences in SP quality and main flavors. This study provides some references for process control and interpretation of heterogeneous mechanisms in low-salt SP fermented by inoculated strains.