A seal structure is provided for an air conditioning unit mounted inside a passenger compartment of a vehicle and connected with pipes, which extends to the passenger compartment from an engine cabin through a pipe penetration opening of an isolation member. The seal structure includes an annular-shape pipe coupling wall formed at a case of the air conditioning unit and arranged at an outer side of a connection unit of the pipes, a first packing unit sandwiched between the pipe coupling wall and the connection unit, and a second packing unit between the isolation member and a front end of the pipe coupling wall. The second packing unit is bonded to both the first packing unit and the pipe coupling wall.