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The in-situ phenotype of sweet pepper is an important reference indicator for fruit breeding and management. Automated measurement of phenotype in-situ through phenotype collection robots is one of the effective ways for digital breeding and management of sweet pepper. However, fruit occlusion during the measurement process seriously affects the success rate of detection. Therefore, a three-dimensional reconstruction method for multi view sweet pepper fruit point cloud was proposed to address the problem of target occlusion in in-situ fruit phenotype measurement. By using the method of virtual leaves, an enhanced dataset was created, and a sweet pepper fruit recognition model based on YOLO v5 algorithm was established to recognize fruits with different degrees of occlusion. At the same time, a fruit phenotype collection algorithm considering fruit position and occlusion degree was constructed to achieve multi view threedimensional data collection of fruits. Finally, the three-dimensional point cloud of sweet pepper fruit was registered, the phenotype parameters of sweet pepper was extracted, and the effectiveness of the point cloud reconstruction method was validated through the greenhouse sweet pepper fruit phenotype. Compared with manual measurement data, the average relative error of fruit width was 1.72%, and the average relative error of fruit height was 1.60%. The experimental results indicated that the in-situ phenotype point cloud reconstruction method proposed for sweet pepper can provide effective solutions and feasible methods for crop phenotypes under occlusion conditions.