To register multiple range images, we present a method for the pose estimation of multiple viewpoints for three-dimensional digital imaging system based on fringe projection. This method illuminates the test object with two orthogonal fringe sequences, respectively, from at least two different viewpoints, then reconstructs Cartesian coordinates of the object in three-dimensional space from phase map with help of fringe projection and phase reconstruction techniques. As the projector can conceptually be regarded as camera acting in reverse, the relation between projection plane of the projector and imaging plane of the camera is fixed. Taking epipolar geometry into account, this approach can further realize the pose estimation of three-dimensional active vision system based on fringe projection. We build up a non linear equation to calculate the parameters of orientation even if the input data are influenced by noise. Mathematical formulation of the proposed method is given and the effectiveness of this approach has been demonstrated by the designed experiments.