Cylinder deactivation (CDA) is an effective technique to improve fuel economy in spark ignition (SI) engines. This technique enhances volumetric efficiency and reduces throttling loss. However, practical implementation is restricted due to torque fluctuations between individual cylinders that cause noise, vibration, and harshness (NVH) issues. To ease torque deviation of the CDA, we propose an in-cylinder pressure based 48V mild-hybrid starter-generator (MHSG) control strategy. The target engine realizes CDA with a specialized engine configuration of separated intake manifolds to independently control the airflow into the cylinders. To handle the complexity of the combined CDA and mild-hybrid system, GT-POWER simulation environment was integrated with a SI turbulent combustion model and 48V MHSG model with actual part specifications. The combustion model is essential for in-cylinder pressure-based control; thus, it is calibrated with actual engine experimental data. The modeling results demonstrate the precise accuracy of the engine cylinder pressures and of quantities such as MAF, MAP, BMEP, and IMEP. The proposed control algorithm also showed remarkable control performance, achieved by instantaneous torque calculation and dynamic compensation, with a 99% maximum reduction rate of engine torque deviation under target CDA operations.