An object is to provide a method and a system of controlling a load during misfire of an engine, whereby additional stress on a crank shaft is calculated from torsional vibration of the crank shaft to obtain an output limit rate, and an operation output of an engine is controlled on the basis of the output limit rate. The method includes: a first step of calculating additional stress on a crank shaft on the basis of a vector sum of crank-shaft torsional vibration vibratory force when the misfire is detected; a second step of determining whether the calculated additional stress on the crank shaft is less than an allowable stress with respect to the crank shaft; a third step of controlling an operation output of the engine to be reduced by a predetermined amount and returning to the first step if the calculated additional stress is greater than the allowable stress and obtaining an output limit rate by calculating the additional stress on the crank shaft if it is determined that the calculated additional stress on the crank shaft is less than the allowable stress with respect to the crank shaft; and a fourth step of controlling the operation output of the engine on the basis of the output limit rate.