The creation of three-dimensional models from an unorganized set of points is an active research area in computer graphics. One of the purposes of this study is to explore the 3D reconstruction of a cube-type artificial reef (CTAR) set by linear structured light and binocular stereo vision technology in an underwater environment. The experimental setup is composed of two cameras in a stereo vision configuration. The alpha shapes method can be used to construct a surface that most closely reflects the artificial reef set described by the points. A parameter study is conducted to assess the scales of the set (i.e., usable volume, surface area, projected area, height, and base diameter) on the basis of 3D reconstruction. Experimental results show that the quality of 3D reconstruction in an underwater environment is acceptable for estimating the scale size of the CTAR set. According to the measurement of the scale sizing of the CTAR set, the relationships between the parameters of the CTAR set and the number of CTAR modules were determined. Moreover, the usable volume of the CTAR set can be estimated depending on the basis of the number of CTAR modules.