The invention provides a water environmental risk source risk representing method in a drainage basin transboundary region. The method is used for evaluating the risk level of a risk source of the drainage basin transboundary region. The risk source of the transboundary region is divided into five categories including a surface source, production enterprises, a centralized treatment place of waste, a chemical storing site and transportation. The method includes the fives steps that first, a risk source risk index system of the transboundary region is constructed, the risk index systems of the five categories of risk sources respectively comprise three first-level indexes and a plurality of second-level indexes, the numbers of the second-level indexes in the risk index systems are different, and the indexes comprise three risk levels of the high risk level, the middle risk level and the low risk level; an information database of the risk sources of the transboundary region is established, values are assigned to all the second-level indexes, and the values of the all the second-level indexes are standardized to [0,1]; then, fuzzy weights of the indexes are determined; next, a fuzzy integration method is adopted for respectively calculating the risk indexes of the risk sources, the self-purification index of environmental mediums, and the vulnerability index of risk receiving bodies; finally, the risk indexes of the risk sources are calculated through the fuzzy integration method so that the risk levels of the risk sources can be represented.