New and useful alignment method and system for electromagnets used in the high energy accelerator that can make the installation simple and less time consuming are disclosed. By measuring the multiple of measurement reference points for obtaining the position and posture information of the electromagnet on the high energy accelerator, the deviation of the present value from the installation target value for the electromagnet within the reference coordinates in the building. For each of the adjustment mechanisms such as the multiple of adjustment bolts or the actuators, the Jacobian matrix representing the relationship between the unit operation amount and the posture changes of the electromagnet is obtained. Then, by calculating operation amounts for each of the adjustment mechanisms through multiplication of the inverse matrix of the Jacobian matrix with the deviation, the position and posture are aligned to the target value by operating the adjustment mechanisms collectively with the calculated operation amounts.