<p>Soil carbon mineralization, alterations in the content of active organic carbon and humus, are the crucial factors contributing to the improvement of soil quality through bio-organic fertilizer application. Nevertheless, the impact of alterations in the carbon composition of each soil humus on carbon mineralization and variations in active organic carbon remains uncertain. In this study, a 3-year field experiment was performed to examine carbon mineralization dynamics, active soil organic carbon, humus fraction, and explore the relationship among them. The treatments consisted of no fertilizer (CK), mineral fertilizer (CF), bio-organic fertilizer (OF), and mineral fertilizer combined with bio-organic fertilizer (COF). The results showed that the application of bio-organic fertilizer (OF and COF) led to the decreases of carbon mineralization (26.4% for OF and 15.9% for COF compared to CF (1299.5&#xa0;mg kg^− 1)). Moreover, fertilization substantially augmented the content of active SOC, especially in the OF treatment. Similarly, higher soil humus carbon was associated with the OF treatment as compared to other treatments. Partial least squares path model analyses elucidated that bio-organic fertilization directly affected humus fraction (<i>P</i> &lt; 0.01), thereby decreasing soil carbon mineralization. Therefore, the results clearly indicated that short-term fertilization using bio-organic fertilizer alone was the optimal choice for enhancing SOC storage and decrease the carbon mineralization.</p>