The drill, codenamed "Tianshan - I (2006)", would be conducted by law enforcement bodies and special services of the two countries, said the ministry.
It would be held in Kazakhstan's eastern Almaty region and the western Chinese city of Yining in Xinjiang Uygur Autonomous Region.
The ministry refused to disclose the number of personnel participating or the specific operations involved.
It would be the first ever joint anti-terrorism exercise between the two countries' law enforcement bodies and special forces within the SCO framework.
It was aimed at implementing the consensus on enhancing security cooperation among member states at the SCO summit in June and to improve coordination between law enforcement departments and special services.
The drill, the third of its kind conducted within the SCO framework, would demonstrate the two states' determination to jointly fight terrorism and maintain security and stability in their border areas.
Observers from the SCO member states and other countries were invited to witness the exercise, said the ministry.
Source: Xinhua