For the purpose of verifying the feasibility of NAPA software in fishing vessel and the accuracy of the stability calculation with the ship's hydrostatical theory, according to the special loading condition of the 49.5m tuna longliner ship, the NAPA software and the table calculation were used respectively. The calculation results showed that the deviation of the two methods was about 2%, which could satisfy the accuracy requirements of the engineering application. About the weather criterion calculation, the Fishing Vessel Statutory Inspection Rules and the International Maritime Organization (IMO) Codes were used respectively. Because of the method difference, the result deviation was a bit large. The comparison results indicated that the requirements of Fishing Vessel Statutory Inspection Rules to weather criterion was stricter than that of the IMO Codes. In the absence of using the large ship calculation software and the ship was untrimmed, the results using the ship's hydrostatical theory were reliable. As the large ship calculation software is used frequently by the designer, so the calculation principle of the NAPA software is necessary for analysis. The ship's hydrostatical theory was adopted and the NAPA calculation model was established. Through the real example calculation, the results showed the feasibility of NAPA software in fishing vessel and the accuracy of the stability calculation with the ship's hydrostatical theory. In addition, the results could provide reference foundation when the ship designer selects different calculation methods.