The invention relates to a method for operating an internal combustion engine (1) provided with at least one working cylinder (3a-3d) each with an associated auxiliary cylinder (5a-5d), which engine (1) is operable in spark ignition and compression ignition modes. Each working cylinder (3a-3d) comprises a working piston (7a-7a) connected to a first crankshaft (9), and each auxiliary cylinder (5a-5d) comprises an auxiliary piston (10a-10d) connected to a second crankshaft (12). The first crankshaft (9) is connected to the second crankshaft (12) to drive the second crankshaft (12) at half the rotational speed of the first crankshaft (9). A device for controlling the phase angle is arranged between the first and second crankshafts. The method involves controlling the phase shift device in order to retain residual exhaust gas and increase the compression ratio. A current combustion phasing timing is determined, and the combustion phasing timing is corrected by increasing or decreasing the phase angle to achieve a desired combustion phasing timing.