Baihetan hydropower station is one the most famous hydroelectric projects in China. The columnar jointed rock mass (CJRM) is widely distributed in this area such as at the dam site and drainage tunnel. The rocks surrounding CJRM are usually unstable due to its discontinuity. Therefore, the investigation of mechanical properties of CJRM is essential to designing relevant structures. In recent years, several previous studies have been conducted to determine the mechanical properties of regular CJRM reconstructed using the mixture of water, cement, and sand. However, few studies have been conducted on the irregular CJRMs formed in nature because of their structural uniqueness. In this study, the mechanical properties of irregular CJRMs reconstructed using 3D printing technology was investigated and verified through laboratory test. First, the sampling window method was adopted to obtain the structural characteristics of columnar jointed basalts (CJBs). After this, the mechanical properties (i.e., uniaxial compressive strength (UCS), uniaxial tensile strength (UTS), peak shear strength, residual shear strength, failure mode, and acoustic emission (AE) characteristics) of the reconstructed and natural CJBs in the laboratory tests were compared based on the similarity constant. The results show that the mechanical properties of irregular CJRM reconstructed using 3D printing are consistent with the in situ specimens when considering the similarity constant. Finally, based on a detailed discussion of the reconstructed and original irregular CJRM, a new method to accurately reconstruct the structure of irregular CJRMs using 3D printing is suggested and verified. This method could be used to design irregular CJRMs in rock engineering.