The cylinder-by-cylinder variations have many bad impacts on the engine performance, such as increasing the engine speed fluctuation, enlarging the torsional vibration and noise. To deal with this problem, the impact mechanism of cylinder-by-cylinder variations on low order torsional vibration has been studied in this paper, and subsequently a new individual cylinder control strategy was designed by processing the instantaneous crankshaft rotation speed signal, detecting the cylinder-by-cylinder variation and using feed-back control. The acceleration characteristics of each cylinder in each engine cycle were compared with each other to extract the variation index. The feed-back control algorithm was based on the regulation of the fuel injection according to the detected variation level. Considering the limited accuracy of ordinary crankshaft signal and the discreteness of sampled signal, an improved variation detection method has been designed to ensure the accuracy of algorithm when implemented in real time operation of the production electronic control unit (ECU). A detailed cylinder-by-cylinder turbocharged engine model has been established to verify the proposed individual cylinder control algorithm, both in off-line simulation and hardware in the loop (HIL) test. A desirable result has been achieved and the precision bound for the algorithm has been discussed.