Storage and dynamics of soil organic carbon (SOC) are the results of input-output balance and soil retention capacity for SOC, which are mainly controlled by bio-climatic conditions, and by soil physiochemical properties such as clay content and soil minerals, respectively. A soil toposequence along an altitudinal gradient was constructed as a natural experiment, aiming to explore the controlling factors for SOC and its fractions in the Qilian Mountains. It is found that soil parent material of this topographic sequence is mainly derived from loess deposits. Chlorite and hydromica are the dominant clay minerals, pointing to the relatively weak chemical weathering intensity of the study region. Meanwhile, the large hydrothermal gradient drives the differences in pedogenic intensities within the topographic sequence. Carbonates exist in soils from the low altitude area; with the rise of altitude, the carbonate is leached away while the contents of iron and aluminum oxide and SOC increase. Further analysis revealed that Al/Fe- oxide was the main explanatory variable for the variance of SOC and its fractions. Partial correlation analysis showed that once the effect of Al/Fe- oxides was controlled, the effects of climate on SOC and its fractions were insignificant. This indicated that the effect of climate on SOC took place mainly via its influence on soil properties, resulting in differences in properties such as Fe and Al oxides. This mechanism mainly occurs in mineral-associated organic carbon (MOC) fraction and make an influence on long-term sequestration of SOC. This study has great implications for understanding the preservation of SOC as well as its responses to climate changes.