In view of the characteristics of river-sea-rail container terminal with multi-shoreline and large depth，combined with the outstanding characteristics and advanced experience of the existing automated container terminals，we put forward a multi-modal automated container terminal handling process scheme，and expound the handling process scheme in detail.The overall layout of the scheme adopts the double U-shaped vertical layout + side handling mode，which realizes the seamless connection of river-sea-rail transport with multi-shoreline berths，and has the advantages of simple traffic organization and high traffic turnover efficiency.It effectively solves the problem that the typical handling system can not adapt the automated container terminal engineering well.