To solve the problem that the exact position relation between three-dimensional lidar and global positioning system/inertial navigation system integrated navigation system cannot be obtained directly and the relative rotation angle between them cannot be directly measured, a method based on simultaneous matching of multiple-point clouds is proposed to calibrate the extrinsic parameters. Firstly, the lidar point clouds, which are similar in position and opposite in direction, are selected as the calibration data. Secondly, we set the parameters of the initial regional center, the initial step length and the step counts, then traverse the combination of parameters to find the optimal target function when the corresponding extrinsic parameters are updated to the optimal iterative regional center. We shorten the step length continuously, until optimal extrinsic parameter that satisfies accuracy requirement is obtained. The experiment collects two different data in different environments, and uses better and worse parameter initial iterative center and different step counts to calibrate. Results show that the proposed calibration method has a short time duration, and can get good calibration results for non-ideal initial parameters. The method is simple, and can achieve required calibration accuracy without special calibration object.