Pareto dominance-based algorithms face a significant challenge in handling many-objective optimization problems. As the number of objectives increases, the sharp rise in non-dominated individuals makes it challenging for the algorithm to differentiate their quality, resulting in a loss of selection pressure. The application of the penalty-based boundary intersection (PBI) method can balance convergence and diversity in algorithms. The PBI method guides the evolution of individuals by integrating the parallel and perpendicular distances between individuals and reference vectors, where the penalty factor is crucial for balancing these two distances and significantly affects algorithm performance. Therefore, a comprehensive adaptive penalty scheme was proposed and applied to NSGA-III, named caps-NSGA-III, to achieve balance and symmetry between convergence and diversity. Initially, each reference vector’s penalty factor is computed based on its own characteristic. Then, during the iteration process, the penalty factor is adaptively adjusted according to the evolutionary state of the individuals associated with the corresponding reference vector. Finally, a monitoring strategy is designed to oversee the penalty factor, ensuring that adaptive adjustments align with the algorithm’s needs at different stages. Through a comparison involving benchmark experiments and two real-world problems, the competitiveness of caps-NSGA-III was demonstrated.