This paper addresses how to define and control the perceived depth when rendering a single stereoscopic three-dimensional (3-D) model. In most 3-D manipulation software, the control of view navigation is the most important feature needed to visualize 3-D scenes of good quality. In a stereoscopic 3-D situation, however, this becomes more complex. We used two factors, parallax range and average parallax, to quantify the 3-D effect of rendering a 3-D model. After an experiment using subjective questionnaires, the fusional limit and depth perception of 22 subjects were regressed as paraboloid functions of parallax range and average parallax. Then, the comfort region, which is defined according to these parameters, was used again for developing an auto-adjustment algorithm for stereoscopic view navigation. This algorithm iteratively adjusts the parameters of a virtual stereo camera and simultaneously restrains parallax range and average parallax within a comfortable region. Finally, by using questionnaires and critical fusion frequency tests, we verified that this algorithm can significantly improve the comfort index of a user in customary operations.