Cropping systems and fertilization have important effects on soil organic carbon (OC) and nitrogen (N) turnover and availability; however, little information exists about the interaction of cropping system and fertilization. Herein, we analyzed the dynamics of soil OC and N in a 31-year experiment in a highland agroecosystem to understand how the effects of fertilization vary with cropping systems. The experiment included different cropping systems, and each system included various fertilization treatments. The cropping systems were continuous alfalfa (Medicago sativa L.), continuous winter wheat (Triticum aestivum L.), and grain-legume rotation of winter wheat + millet (Panicum miliaceum L.) - pea (Pisum sativum L.) - winter wheat. The fertilization treatments were the control (CK), phosphorous (P), P and nitrogen (NP) and NP and manure (NPM). A bare fallow treatment that did not receive any crop and fertilizer was designed to compare the effects of the cropping systems. The soil samples were collected at different times of the experiment. The contents of OC, N, and labile OC were measured, and the carbon management index was calculated. When averaged across the experimental periods, soil OC, N, labile OC and carbon management index were significantly higher in the pure legume (i.e., continuous alfalfa) system than in the bare fallow and nonlegume system (i.e., continuous winter wheat) due to the higher C and N inputs from root biomass. The NP and NPM significantly increased these soil variables, and the effects of NPM were greater than those of NP due to the higher supplying of C and N in NPM treatment than NP treatment. However, the effects of NP or NPM on soil OC and N contents were similar among the cropping systems. The effects of P were greater in the continuous alfalfa system but smaller in the continuous winter wheat system in comparison with those in the grain-legume rotation system. Therefore, at the conditions of our study, legume-included cropping systems with large root biomass and manure combined with chemical fertilizers have the potential to increase OC and N and their availability in highland soils, which could be important strategies for improving soil fertility and quality and sequestrating C in soils. Moreover, P fertilizer was recommended for the legume-included cropping systems.