A method and system for controlling computer operation time is provided for counting how long the time for using the computer lasts. The steps of the time counting method are as following. First step is counting an operation time period for using the computer at the computer powered on; second step is determining the operation time period equal to a predetermined operating-time limit; third step is controlling the computer into an interrupted operating state when the operation time period is equal to the predetermined operating-time limit, wherein an interrupted time period for the computer stayed in the interrupted operating state is counted; fourth step is determining the interrupted time period equal to a predetermined suspension time; and fifth step is controlling the computer back to a normal operating state when the interrupted time period is equal to the predetermined suspension time, wherein the operation time period is re-counted.