In order to improve the accuracy, efficiency and automatic degree of existing acquisition techniques of animal’s conformation, based on two depth cameras, a real time system which can reconstruct the animal for body measurement, an automatic ball target based method for the extrinsic calibration of reconstruction system which is based on RANSAC were put forward. The extrinsic parameters can be used for registering point clouds acquired synchronously from depth camera in real time. And then, interactive measuring method which is optimized in picking mode for body measurement was used to get shape traits of animal. Xtion PRO was chosen as data acquisition equipment, and taking the pig specimen as an example, point clouds data acquired from high precision laser scanner was applied to evaluation of the system. The results show that the ball-target-based method can get the extrinsic parameters of depth camera automatically; the average error of registered data is less than 7.50mm; the speed of reconstructing the whole pig can reach in excess of 15f/s; body measurement error is less than 4%. So the system can be applied to body measurements in agricultural field.