A control system for an electric bike includes a controller which has a first Bluetooth transmitting unit connected to a mobile device by a wireless way. The mobile device includes a second Bluetooth transmitting unit, a detector and an operation application. The user calls a learning application which learns the operation application that currently operates the bike in different situations, and then the learning application takes over the control of the bike, Therefore, the user does not need a hand to operate the mobile device to control the bike.