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 losing. Each of R-LAT emits two nonparallel laser planes to scan the measurement space via evenly rotation, while the photoelectric sensors receive these laser planes signals and performs the coordinate calculation based on triangulation. The accurate geometric parameters of the two laser planes plays a crucial role in maintaining the measurement precision of R-LAT system. Practically, the geometry of the two laser plane, which is termed as intrinsic parameters, is unknown after assembled. Therefore, how to figure out the accurate intrinsic parameters 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 with adopting coordinate measurement machine. The mathematic 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 minimize the sum of deviations of target points and laser planes, and the ascertain 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 on the accuracy of intrinsic parameters.