Confronting the financial turmoil, the international liner shipping industry is turning to sea-rail through transport business strengthening for new profit increasing. Traditional studies on empty container repositioning problem are mainly focused on that between seaports of call of container lines, with less effort on sea-land, especially sea-rail through transport. This study analyzes in detail characteristics of container movement under sea-rail through transport, sets up reasonable mathematical model, and its conclusions are of benefit to the improvement of empty container repositioning efficiency and the decrease of costs thereof for existing container lines both theoretically and practically.