The zero-energy building (ZEB) concept has a high potential for securing energy savings in the building sector. To achieve ZEB, various active systems, including renewable systems such as photovoltaic, solar heating, and geothermal systems, have been developed. However, the existing systems are costly or not optimized. To overcome these issues, the authors previously developed an integrated tri-generation system. In this research, the previously developed system was comprehensively analyzed considering the indoor thermal comfort and energy efficiency to develop a design and operation method for the integrated system. Two different heating systems (convective heating and radiant floor heating) were employed in the tri-generation system, and their system performance, predicted mean vote (PMV), and predicted percentage of dissatisfied (PPD) were compared using simulations. The results showed that the heating coefficient of power of the radiant floor heating system was 18.8% higher than that of the convective heating system. Moreover, the radiant floor heating system (Case 4) met the PMV and PPD standards during all the heating periods. Overall, radiant floor heating was found to be more efficient than convective heating. The results confirm that radiant floor heating is more suitable than convective heating considering the indoor thermal comfort of occupants.