Long-term application of high nitrogen and phosphorus fertilizer and mono-tillage practices can adversely affect soil health, carbon sequestration and crop growth. A 10-year field experiment was conducted in a wheat-maize cropping system on the Loess Plateau in China to explore fertilization and tillage methods that improve SOC sequestration and crop yields. We evaluated the effects of (1) fertilization (balanced fertilization (BF), low fertilization (LF), and conventional fertilization (CF)) and (2) alternating years of different tillage (no-tillage and subsoiling (NS), subsoiling and ploughing (SP), ploughing and no-tillage (PN)) or continuous ploughing tillage (PP) on input-C, SOC pool, and crop yields. BF and rotational tillage (NS, SP, and PN) increased the amount and stabilization rate of input-C, thereby increased SOC storage, and the highest effect was found in BF+NS treatment. Simultaneously, BF produced higher contents of SOC, readily oxidizable carbon (ROC), particulate organic carbon (POC) and dissolved organic carbon (DOC) and C pool management index (CMI) at 0-10 cm depth. For tillage, rotational tillage increased labile C contents and CMI at 0-10 cm, 20-35 cm and 35-50 cm depths, which improved soil quality. Crop yields showed an increase tendency with the increases of SOC content, labile C fraction contents, and CMI. Therefore, the higher yields of wheat and maize were found in BF and rotational tillage; the highest were in BF+NS treatment. Our finding suggested that NS combined with BF may be the best management to increase SOC storage, improve soil quality and productivity on China’s Loess Plateau.