In large-scale water conservancy and hydropower projects, complex rock structures are considered to be the main factor controlling the stability of hydraulic structures. The classification of rock mass structure plays an important role in the safety of all kinds of large buildings, especially underground engineering buildings. As a quantitative classification index of rock mass, the rock block index is very common in the classification of borehole and dam foundation rock mass structures. However, there are few studies on the classification of underground engineering rock masses. Moreover, their classification criteria have disadvantages in spatial dimension. Therefore, this paper takes the long exploratory cave CPD1 in the water transmission and power generation system of the Qingtian pumped storage power station in Zhejiang Province as the research object and launches a study on the structural classification of the rock mass of a flat cave based on the 3D rock block index. According to the group distribution of joints, the sections are statistically homogeneous. Additionally, the Monte Carlo method is used to carry out random simulations to generate a three-dimensional joint network model. The virtual survey lines are arranged along the center of the shape of the three different orthogonal planes of the 3D joint network model to represent the boreholes, and the RBI values of the virtual survey lines on each orthogonal plane are counted to classify the rock mass structure of the flat cave in a refined manner using the rock block index of the rock mass in 3D. The above method realizes the application of the 3D rock block index in underground engineering and overcomes the limitations of traditional rock mass classification methods in terms of classification index and dimension. The results show that: (1) Three-dimensional joint network simulations built on statistical and probabilistic foundations can visualize the structure of the rock mass and more accurately reflect the structural characteristics of the actual rock mass. (2) Based on the 3D rock block index, the rock mass structure of the long-tunnel CPD1 is classified, from that of a continuous structure to a blocky structure, corresponding to the integrity of the rock mass from complete to relatively complete. The classification results are consistent with the evaluation results of horizontal tunnel seismic wave geophysical exploration. (3) Based on the 3D joint network model, it is reasonable and feasible to use the 3D rock block index as a quantitative evaluation index to determine the structure type of flat cave rock masses. The above method is helpful and significant in the classification of underground engineering rock mass structures.