This paper suggests a relative orbit control strategy for the CubeSat Astronomy by NASA and Yonsei using Virtual Telescope Alignment eXperiment (CANYVAL-X) mission whose main goal is to demonstrate an essential technique, which is an arrangement among two satellites and a specific celestial object, referred to as inertial alignment, for a next-generation virtual space telescope. The inertial alignment system is a relative orbit control system and has requirements for the relative state. Through the proposed orbit control strategy, consisting of separation, proximity keeping, and reconfiguration, the requirements will be satisfied. The separation direction of the two CubeSats with respect to the orbital plane is decided to provide advantageous initial condition to the orbit controller. Proximity keeping is accomplished by differential atmospheric drag control (DADC), which generates acceleration by changing the spacecraft’s effective cross section via attitude control rather than consuming propellant. Reconfiguration is performed to meet the requirements after proximity keeping. Numerical simulations show that the requirements can be satisfied by the relative orbit control strategy. Furthermore, through numerical simulations, it is demonstrated that the inertial alignment can be achieved. A beacon signal had been received for several months after the launch; however, we have lost the signal at present.