An apparatus for controlling exhaust gas purification may include a front unit communicating with an engine exhaust pipe and having a first catalytic filter; a rear unit communicating with the front unit through a connection pipe and having a second catalytic filter and a bypass channel formed to surround the second catalytic filter; and an actuator to open or close the bypass channel. In particular, one end of the bypass channel is opened or closed and other end thereof is sealed so that the second catalytic filter is heated by a primary filtered exhaust gas filtered by and discharged from the front unit.