Taking the typical yellow soil in Guizhou as the research object, four treatments were set up: no fertilization (CK), single application of chemical fertilizer (NP), 50% organic fertilizer instead of chemical nitrogen fertilizer [1/2(NPM)], and 100% organic fertilizer instead of chemical nitrogen fertilizer (M). The effects of organic fertilizer instead of chemical nitrogen fertilizer on organic carbon and its active components, soil carbon pool management index, soil enzyme activity, and maize and soybean yield in yellow soil were studied in order to provide theoretical basis for scientific fertilization and soil quality improvement in this area. The results showed that the replacement of chemical nitrogen fertilizer by organic fertilizer significantly increased soil pH, organic carbon (SOC), total nitrogen (TN) content, and C/N ratio. Compared with those in the CK and NP treatments, the content and distribution ratio of soil active organic carbon components and soil carbon pool management index (CPMI) were improved by replacing chemical nitrogen fertilizer with organic fertilizer, and the effect of replacing chemical nitrogen fertilizer with 50% organic fertilizer was the best. Compared with those in the NP treatment, the 1/2 (NPM) treatment significantly increased the contents of soil readily oxidizable organic carbon (ROC333, ROC167), dissolved organic carbon (DOC), and microbial biomass carbon (MBC) by 22.90%, 8.10%, 29.32%, and 23.22%, respectively. Compared with those under the CK and NP treatments, organic fertilizer instead of chemical nitrogen fertilizer increased soil enzyme activities. The activities of catalase, urease, sucrase, and phosphatase in the 1/2 (NPM) treatment were significantly increased by 21.89%, 8.24%, 34.91%, and 18.78%, respectively, compared with those in the NP treatment. Compared with that of the NP treatment, the maize yield of the 1/2 (NPM) and M treatments was significantly increased by 44.15% and 17.39%, respectively. There was no significant difference in soybean yield among different fertilization treatments. Correlation analysis showed that soil SOC was significantly positively correlated with ROC333, ROC167, ROC33, DOC, MBC, and soil active organic carbon components, and CPMI was significantly positively correlated with soil organic carbon and its active components (P<0.01). Corn yield was significantly positively correlated with soil enzyme activity, CPMI, total organic carbon, and its active components (P<0.05). Therefore, from the perspective of yield increase and soil fertility, 50% organic fertilizer instead of chemical nitrogen fertilizer was conducive to improving soil quality and soil fertility, which is the key fertilization technology to achieve a high yield of crops in the yellow soil area of Anshun, Guizhou.