A casing structure and a locking mechanism thereof for portable electronic apparatus are disclosed. The casing structure includes an apparatus casing, an electronic device casing, and a door. The electronic device casing is engaged to the apparatus casing in a detachable way. The door is engaged to the apparatus casing in an open-able way to cover an open of the apparatus casing. The locking mechanism is mainly disposed on the apparatus casing and can be operative to lock or unlock the electronic device casing and the door simultaneously. Thereby, a user can quickly detach the electronic device casing and open the door to maintain or replace components in the apparatus casing, which avoids the complicated operation of opening the casing in the prior art.