The invention discloses an important water functional area water quality risk evaluation method based on multi-source data coupling, and the method comprises the steps: dividing a water functional area into a plurality of water functional area control units, and carrying out the sensitivity evaluation of the control units; positioning a pollution source in the water functional area and evaluatingthe pressure of the pollution source; based on the evaluation result, grading pollution source risk in the water functional area control unit; assigning values to risk sources of different levels, substituting the values as input conditions into the river, lake and reservoir one-dimensional steady-state mixed attenuation model to obtain a water system risk field index of each water functional areacontrol unit, and distributing the risk field indexes to the area according to the range of the water functional area control units to obtain a water functional area water quality risk map. Factors such as sensitivity of a water functional area, pollution source pressure and a water system risk field are comprehensively considered, the complete process of risk substance generation, transportationand influence on an accepted object is monitored, and all key processes are quantified by establishing a multi-index evaluation system and a steady-state model.