The present invention discloses an encrypted remote connection-based remote terminal unit maintenance system. The encrypted remote connection-based remote terminal unit maintenance system comprises an operation and maintenance engineer station, a longitudinal encryption authentication device, a router and a maintenance computer; the operation and maintenance engineer station deployed in an adjustment and control center establishes a remote connection from the adjustment and control center to a router and to the maintenance computer in a transformer substation; the longitudinal encryption authentication device performs tunnel encryption on the remote connection and filters other network connections and messages; and the maintenance computer arranged in the in the transformer substation receives the instructions of the operation and maintenance engineer station through the encrypted remote connection so as to complete the maintenance work of a remote terminal unit. With the system adopted, remote maintenance on the remote terminal unit in the transformer substation can be performed in the adjustment and control center, and time and labor costs can be saved. The invention also discloses an encrypted remote connection-based remote terminal unit maintenance method.