The present investigation was conducted during 2015-2016 under ongoing All India Coordinated Research Project on LTFE with soybean-safflower cropping sequence in Vertisol (Typic Haplusters) that commenced from 2006-2007 at Vasantrao Naik Marathwada Krishi Vidyapeeth, Parbhani. The present investigation was conducted to study the continuous effect of long-term organic manure and fertilizers on soil organic carbon pools under soybean-safflower cropping system. Treatment includes 50% NPK, 100% NPK, 150% NPK, 100% NPK + hand weeding, 100% + ZnSO4 at 25 kg ha-1, 100% NP, 100% N, 100% NPK + FYM at 5 Mg ha-1, only FYM, absolute control, fallow. The experiment was laid out in Randomized Block Design (RBD) with twelve treatments and four replications. Continuous application of organic manure alone... or in combination with inorganic fertilizer significantly influenced the soil organic carbon, water soluble carbon, labile carbon, total organic carbon, dehydrogenase activity, carbon management index. The active fraction of soil organic carbon significantly higher in plot receiving 100% NPK + FYM at 5 Mg ha-1. Significantly increase in soil organic carbon (6.89 g kg-1), water soluble carbon (26.93 mg kg-1), and labile carbon (325.50 mg kg-1) with the application of 100% NPK + FYM at 5 Mg ha-1. Integrated use of nutrient sources was significantly increases dehydrogenases activity (50.21 µg g-1 soil 24 hr-1), total carbon content (18.76 g kg-1) in treatment receiving 100% NPK + FYM at 5 Mg ha-1 and in treatment receiving 150% NPK and only FYM 10 Mg ha-1. As compared to no-fertilizer and no-manure application (control), the carbon management index (CMI) was 2.24 fold higher when organic and inorganic fertilizer applied 100% NPK + FYM at 5 Mg ha-1 improvement in the plant stand and increase in organic inputs increase in CMI would serve as better indicator for soil health. Integrated use of FYM with chemical fertilizers or FYM alone exerted significant effect on soil organic carbon pools in soil.