As a necessary structure for the construction of hydropower stations, the crane beam of reinforced concrete powerhouse is widely used in the dam engineering. However, the environmental conditions of low temperature, high wind speed and low humidity in the alpine regions easily lead to irregular surface cracks in the reinforced concrete crane beam during construction, which seriously affects the safe service of the concrete structure. The scale of irregular cracks is much smaller than the structural scale of reinforced concrete crane beams, which makes it difficult for the existing calculation methods to effectively consider the irregularity and morphological authenticity of the cracks. To solve this problem, a highly detailed simulation method for irregular cross-scale cracks based on real crack point cloud is proposed. In this method, the crack surface is represented by point clouds and embedded to the finite element meshe of the structure. The element nodes where the crack passes through are then projected to the crack surface in batches to capture the crack and its propagation path. The main advantage of the proposed method is that it does not need to change the initial element types and mesh the geometric model with cracks, which can reduce the difficulty of meshing for complex 3D models and is more applicable than conventional geometric subdivision method. Moreover, the concrete three-point bending beam and wedge-splitting experiments are conducted to verify this proposed method. Then this method is applied to the structural safety analysis of a reinforced concrete crane beam in the alpine region of China, which can provide a technical support for the subsequent quality assessment and reinforcement of crane beams.