Carbon is the crucial source of energy during aerobic composting. There are few studies that explore carbon preservation by inoculation with microbial agents during goat manure composting. Hence, this study inoculated three proportions of microbial agents to investigate the preservation of carbon during goat manure composting. The microbial inoculums were composed of Bacillus subtilis, Bacillus licheniformis, Trichoderma viride, Aspergillus niger, and yeast, and the proportions were B1 treatment (1:1:1:1:2), B2 treatment (2:2:1:1:2), and B3 treatment (3:3:1:1:2). The results showed that the contents of total organic carbon were enriched by 12.21%, 4.87%, and 1.90% in B1 treatment, B2 treatment, and B3 treatment, respectively. The total organic carbon contents of B1 treatment, B2 treatment, and B3 treatment were 402.00 ± 2.65, 366.33 ± 1.53, and 378.33 ± 2.08 g/kg, respectively. B1 treatment significantly increased the content of total organic carbon compared with the other two treatments (p < 0.05). Moreover, the ratio of 1:1:1:1:2 significantly reduced the moisture content, pH value, EC value, hemicellulose, and lignin contents (p < 0.05), and significantly increased the GI value and the content of humic acid carbon (p < 0.05). Consequently, the preservation of carbon might be a result not only of the enrichment of the humic acid carbon and the decomposition of hemicellulose and lignin, but also the increased OTU amount and Lactobacillus abundance. This result provided a ratio of microbial agents to preserve the carbon during goat manure aerobic composting.