Drought is one of the most frequent meteorological disasters, and has exerted significant impacts on the livelihoods and economy of the Koshi River Basin (KRB). In this study, we assessed drought patterns using the Crop Water Shortage Index (CWSI) based on the MOD16 product for the period between 2000 and 2014. The results revealed that the CWSI based on the MOD16 product can be act as an indicator to monitor the characteristics of the drought. Significant spatial heterogeneity of drought was observed in the basin, with higher CWSI values downstream and upstream than in the midstream. The midstream of the KRB was dominated by light drought, moderate drought occurred in the upstream, and the downstream was characterized by severe drought. The monthly CWSI during one year in KRB showed the higher CWSI between March to May (pre-monsoon) and October to December (post-monsoon) rather than June to September (monsoon), and the highest was observed in the month of April, suggesting that precipitation plays the most important role in the mitigation of CWSI. Additionally, the downstream and midstream showed a higher variation of drought compared to the upstream in the basin. This research indicates that the downstream suffered severe drought due to seasonal water shortages, especially during the pre-monsoon, and water-related infrastructure should be implemented to mitigate losses caused by drought.