This research proposed a novel shape design by integrating the geometry that showed the best performance including fin length, pitch and angle on the high temperature heat exchanger of Stirling engine designed for the prime mover of 1kW cogeneration system for home. First, the numerical simulation was conducted on the new design and existing shape, and the performance improvement according to the shape optimization was checked. Next, the validity of its performance was verified by additionally considering the heat loss from the recuperation and low-temperature heat exchanger. As a result, when the high temperature heat exchanger is optimized, a great amount of heat quantity is absorbed from the fuel gas from the upstream part where negative heat flux occurred in the cylinder head part. This was judged to be because of the fixed temperature of the high-temperature part in the thermodynamic cycle. Thus, when researching the shape of the high-temperature heat exchanger, an optimized geometry can be obtained when combining cycle interpretation of system rather than interpreting independently.