Disclosed is a method and system for estimating an adaptive joint channel in a CDMA system based on TDD. The method includes the steps of a) receiving activity information of a mobile terminal; b) parsing the activity information, and transmitting a midamble sequence to the mobile terminal when a result of the parsing shows that the mobile terminal is in an ON state; c) conducting adaptive joint channel estimation by using the midamble sequence in the mobile terminal; and d) conducting adaptive joint detection by using a channel impulse response of the mobile terminal, obtained as a result of conducting the adaptive joint channel estimation. The method and system decreases the complexity in channel estimation and additionally increases the accuracy of channel estimation by reducing transmission power consumption and eliminating unnecessary interference.