Abstract: In this paper,the authors aim to clarify the spatio-temporal patterns of cloud interference in Dongjiang River basin and then provide scientific basis for vegetation index studies at the level of higher precision in this area. Cloud flag information of MOD13Q1 product data sets within the range of Dongjiang River basin from 2001 to 2015 were analyzed using the GIS approach. Three aspects were analyzed,i.e.,the probability of cloud interference and its spatial distribution, the elimination rate of cloud interference and its spatial distribution and the seasonal differences of cloud interference duration period length. The results show that the whole probability of cloud interference was reduced rapidly with the increase of compounding period length,the new added elimination rate of cloud interference firstly increased and then decreased with the increase of compounding period length. The duration period length of cloud interference was relatively longer in southern urbanized region,and in summer and spring. The results of this study can provide scientific basis for choosing or developing better methods of removing clouds for vegetation index time-series data.