The invention discloses a method for controlling vibration of a flexible manipulator based on a vibration observer. The method comprises the following steps: 1, establishing a mathematic model of a flexible manipulator system and acquiring model information of the system; 2, designing the vibration observer; 3, designing a state feedback integral controller; 4, adjusting control parameters according to the combined simulation effect; 5, ending the design. When the residual vibration of the tail end of the flexible manipulator is tested and controlled, a vibration signal of the tail end of the flexible manipulator can be obtained without using a sensor in an existing method, the system structure is simplified, and the cost is saved. The state feedback controller with an integral is used at the same time, and unbiased tracked and specified input can be achieved while the dynamic characteristics of the system are effectively adjusted.