In a spark ignition engine, a variable valve lift (VVL) system has been developed for high fuel efficiency and low power loss. However, changes in valve lift cause deviations of cylinder air charge which lead to individual cylinder equivalence ratio maldistribution. In this study, in order to reduce the maldistribution, we propose individual cylinder equivalence ratio estimation and control algorithms. The estimation algorithm calculates the equivalence ratio of each cylinder by using a mathematical engine model which includes air charging, fuel film, exhaust gas, and universal exhaust gas oxygen sensor (UEGO) dynamics at various valve lifts. Based on the results of estimated equivalence ratio, the injection quantity of each cylinder is adjusted to control the individual cylinder equivalence ratio. Estimation and control performance are validated by engine experiments. Experimental results represented that the equivalence ratio maldistribution and variation are decreased by the proposed algorithms.