The long-term overuse of fertilizers negatively affects soil chemical properties and health, causing unsustainable agricultural development. Although many studies have focused on the effects of long-term fertilization on soil properties, few comparative and comprehensive studies have been conducted on fertilization management over the past 35 years in China. This meta-analysis (2058 data) evaluated the effects of the fertilizer, climate, crop types, cultivation duration and soil texture on the soil chemical properties of Chinese croplands. NPKM (NPK fertilizers + manure) led to the highest increase in pH (−0.1), soil organic carbon (SOC) (+67%), total nitrogen (TN) (+63%), alkali-hydrolysable nitrogen (AN) (+70%), total phosphorus (TP) (+149%) and available potassium (AK) (+281%) compared to the unfertilized control, while the sole nitrogen fertilizer (N) led to the lowest increase. The SOC (+115%) and TN (+84%) showed the highest increase under the influence of NPKM in an arid region. The increase in the chemical properties was higher in unflooded crops, with the maximum increase in the wheat–maize rotation, compared to rice, under NPKM. The SOC and TN increased faster under the influence of organic fertilizers (manure or straw) compared to mineral fertilization. Fertilizers produced faster effects on the change in the SOC and TN in sandy loam compared to the control. Fertilizers showed the highest and lowest effects on change in pH, organic C to total N ratio (C/N), TP and TK in clay loam with the cultivation duration. NPKM greatly increased the C/N compared to NPK in an arid region by 1.74 times and in wheat by 1.86 times. Reaching the same SOC increase, the lowest TN increase was observed in wheat, and the lowest increase in TP and AK was observed in rice, compared to the other crops. These results suggest that organic fertilizers (manure or straw) play important roles in improving soil fertility and in acidification. NPKM greatly increased the potential for soil C sequestration in wheat and in the arid region. The small increases in TP and TK can increase the SOC in rice and in the humid region. Therefore, considering the crop types and climatic conditions, reduced fertilization and the combination of mineral fertilizers with manure may be the best ways to avoid agricultural soil deterioration and increase soil carbon sequestration.