The present invention has been made to solve the foregoing problems and it is an object of the present invention to provide a two-layer flow air conditioning system in which a partition wall is installed on a path between an evaporator and a heater core to divide internal air and external air, and a first temperature adjusting door and a second temperature adjusting door each having a fan shape are installed at both sides of the partition wall in such a manner as to be opened at their sides to control the flow direction of the internal air and the external air which are supplied to both sides of the partition wall so as to prevent any mixture between the internal air and the external air, thereby enhancing heating and cooling effects without degrading a defrosting performance. It is another object of the invention to provide a two-layer flow air conditioning system in which a first temperature adjusting door and a second temperature adjusting door is operated separately and a horizontal partition wall extends from the rearward of the evaporator to the rearward of a heater core via the heater core so that the cool and warm air having different properties is circulated through separate passages to supply the warm air to the vehicle interior and supply the cool air to a windshield for defrosting or to supply the cool air to the vehicle interior and supply the warm air is supplied to the windshield.