In this paper, in order to handle the high nonlinearity and the sophisticated disturbance in marine engines, a variable sampling rate based active disturbance rejection controller is developed for engine speed control. In the proposed method, the Active Disturbance Rejection Control (ADRC) is designed with the consideration of the practical application in engine speed control that is known as the Crank-angle (CA) based or event-based sampling and control, which means the sampling interval varies with the engine speed. Such a problem has not been discussed in any previous study regarding the application of ADRC in engine control. To this end, this paper discusses the convergence of the variable sampling rate based Extended State Observer (ESO), as well as its parameters that guarantee stability. To verify the proposed control scheme more properly, a cycle-detailed hybrid nonlinear engine model is employed. Finally, simulations are carried out on the Hardware-in-the-loop (HIL) system to assess the superiority of the proposed strategy. The comparative results with a Fuzzy-Proportional-Integral-Derivative (PID) controller demonstrate that the proposed control scheme has better adaptation to engine speed, load disturbances, and stronger robustness towards model uncertainties, which indicates a promising reduction of time and burden for calibrating the controller. It also proved that the proposed CA based ADRC by variable sampling rate method outperforms the general fixed sampling rate ADRC, which is widely used in previous works. Moreover, the successful application of the proposed algorithm via CA based strategy in a real Engine Control Unit (ECU) indicates its huge potential in practical engine control.