Japan faces the risk of huge earthquakes such as the Nankai trough giant earthquake and earthquake centered directory under the capital. These earthquake could cause huge damage to human and property. However, long-term economic damage of GDP caused by these earthquake are not sufficiently predicted. Therefore, in this research, we try to estimate long-term economic damage caused by the Nankai trough giant earthquake and earthqouake centered directory under the capital. As a result, the 20-year economic damage coused by the Nankai trough giant earthquake and earthqouake centered directory under the capital are estimated to be 1048 trillion yen and 678 trillion yen, respectively.