Understanding the effect of the environment, crop types, and land management practices on the organic carbon sequestration of top soil is crucial for adopting management strategies in highland agricultural areas. The objectives of this study are: (1) to estimate top soil organic carbon density (SOCD) of different crop types and (2) to analyze the factors controlling top SOCD in highland agricultural areas. The top soil layers from 0 to 30 cm depths were collected from the Mae Chaem basin, Northern Thailand. The results showed that the highest top SOCD was found soil used for growing upland rice, which contained an average of 58.71 Mg C ha−1. A significant difference between the top SOCD was detected between areas where minimum tillage and conventional tillage of various crops, with average of values 59.17 and 41.33 Mg C ha−1, respectively, for areas growing strawberries; 61.14 and 37.58 Mg C ha−1, respectively, for cabbage, and 71.15 and 39.55 Mg C ha−1, respectively, for maize. At higher elevation, the top SOCD was high, which may be due to high clay content and low temperature. Increased use of chemical fertilizers lead to increases in top SOCD, resulting in increased crop yields. Elevation, bulk density, N and K2O fertilizers were the main factors controlling the top SOCD at all sites.