The interaction between cardiovascular system and the respiratory system is complicated and may be used for the rehabilitation of the cor pulmonale disease. To study the effects of different breathing mode on the cardiac and pulmonary systems, a mathematical model is established based on the previous work. Using this model, computer simulation experiments are carried out for searching an optimal respiration mode in treating of cor pulmonale disease. Results indicate that the step-leap respiration mode could provide a better assistant to the rehabilitation of the cor pulmonale patients in the sense of increasing coronary flow, reducing pulmonary arterial pressure and reducing the working load for the right heart. This result is also proven by the clinical experiments. This work may suggest that a proper directed respiration exercise can be used in the treatment of cor pulmonale disease.