Partial fuel stratification (PFS) is a promising fuel injection strategy to improve the stability of lean combustion by applying a small amount of pilot injection right before spark timing. Mixed-mode combustion, which makes use of end-gas autoignition following conventional deflagration-based combustion, can be further utilized to speed up the overall combustion. In this study, PFS-assisted mixed-mode combustion in a lean-burn direct injection spark-ignition (DISI) engine is numerically investigated using multi-cycle large eddy simulation (LES). A previously developed hybrid G-equation/well-stirred reactor combustion model for the well-mixed operation is extended to the PFS-assisted operation. The experimental spray morphology is employed to derive spray model parameters for the pilot injection. The LES-based model is validated against experimental data and is further compared with the Reynolds-averaged Navier–Stokes (RANS)-based model. Overall, both RANS and LES predict the mean pressure and heat release rate traces well, while LES outperforms RANS in capturing the cycle-to-cycle variation (CCV) and the combustion phasing in the mass burned space. Liquid and vapor penetrations obtained from the simulations agree reasonably well with the experiment. Detailed flame structures predicted from the simulations reveal the transition from a sooting diffusion flame to a lean premixed flame, which is consistent with experimental findings. LES captures more wrinkled and stretched flames than RANS. Finally, the LES model is employed to investigate the impacts of fuel properties, including heat of vaporization (HoV) and laminar burning speed (SL). Combustion phasing is found more sensitive to SL than to HoV, with a larger fuel property sensitivity of the heat release rate from autoignition than that from deflagration. Moreover, the combustion phasing in the PFS-assisted operation is shown to be less sensitive to SL compared with the well-mixed operation.