Embodiments of an apparatus and method for controlling system operation based on battery state are provided. The apparatus includes a first memory for storing an operating system (OS) to operate and control the system, a microcomputer for controlling the system operation based on battery discharge/charge state information, and a second memory for storing an application containing a microcomputer interface information to control the system operation that is changed depending on the battery state under the OS. An operation based on battery residual quantity is set to an operating system (OS) and a microcomputer. Then, if a user changes operation information based on the battery residual quantity, the changed operation information is applied to the microcomputer through at least one of the OS and an application, and the system is operated based on the changed operation system.