Land use and cover change (LUCC) is an important indicator of the human-earth system under climate/environmental change, which also serves as a key impact factor of carbon balance, and a major source/sink of soil carbon cycles. The Heihe River Basin (HRB) is known as a typical ecologically fragile area in the arid/semi-arid regions of northwestern China, which makes it more sensitive to the LUCC. However, its sensitivity varies in a broad range of controlling factors, such as soil layers, LUCCs and calculation methods (e.g. the fixed depth method, FD, and the equivalent mass method, ESM). In this study, we performed a meta-analysis to assess the response of soil organic carbon (SOC) and total nitrogen (TN) storage to the LUCC as well as method bias based on 383 sets of SOC data and 148 sets of TN data from the HRB. We first evaluated the calculation methods and found that based on the FD method, the LUCC caused SOC and TN storage to decrease by 17.39% and 14.27%, respectively; while the losses estimated using the ESM method were 19.31% and 18.52%, respectively. The deviations between two methods were mainly due to the fact that the FD method ignores the heterogeneity of soil bulk density (BD), which may underestimate the results subsequently. We then analyzed the response of SOC and TN storage to various types of the LUCC. In particular, when woodland and grassland were converted into cultivated land or other land types, SOC and TN suffered from heavy losses, while other LUCCs had minor influences. Finally, we showed that increasing the depth of the soil layers would reduce the losses of SOC and TN storage. In summary, we identified a series of controlling factors (e.g. soil layer, the LUCC and calculation method) to evaluate the impact of the LUCC on SOC and TN storage in the HRB, which should be considered in future research.