Rotary-laser automatic theodolite (R-LAT) system is a distributed large-scale metrology system, which provides parallel measurement in scalable measurement room without obvious precision loss. Each of R-LAT emits two nonparallel laser planes to scan the measurement space via evenly rotations, while the photoelectric sensors receive these laser plane signals and perform the coordinate calculation based on triangulation. The accurate geometric parameters of the two laser planes play a crucial role in maintaining the measurement precision of R-LAT system. In practice, the geometry of the two laser planes, which is termed as intrinsic parameters, is usually unknown after assembled. Therefore, how to figure out the accurate intrinsic parameter of each R-LAT is a fundamental question for the application of R-LAT system. This paper proposed an easily operated intrinsic parameter calibration method for R-LAT system by adopting coordinate measurement machine. The mathematical model of laser planes and the observing equation group of R-LAT are established. Then, the intrinsic calibration is formulated as a nonlinear least-square problem that minimizes the sum of deviations of target points and laser planes, and the ascertainment of its initial guess is introduced. At last, experience is performed to verify the effectiveness of this method, and simulations are carried out to investigate the influence of the target point configuration in the accuracy of intrinsic parameters.