The 2011 off the Pacific coast of Tohoku Earthquake and the 2016 Kumamoto Earthquake have increased the interest in the seismic hazard assessment. As new knowledge has been revealed with every new major earthquake, it is important to consider the range of the uncertainty of the parameters which are needed to the assessment and to understand the impact of each earthquake by probabilistic seismic hazard analysis, in advance. The Ikata SSHAC project is the first attempt in Japan to apply SSHAC Level 3 to the probabilistic seismic hazard analysis. In this paper, we report on the results of the modeling of various seismic sources, which include the Median Tectonic Line fault zone which is a long active fault and trench earthquakes occurring in the Nankai Trough. In addition, we discuss the effectiveness of guidelines for SSHAC Level 3, the range of the uncertainty and on the impact on the seismic hazard, because the gained knowledge and know-how of the scope would be useful for subsequent studies.