Operational parameters of a Tunnel Boring Machine (TBM) under different geological properties have significant influence on muck removal performance. To improve the muck removal performance for Yinsong Tunnel TMB, tuff and granite properties were surveyed by geological detection in the tunnel project, and the optimization of advancement and rotational speed of cutterhead was investigated. The muck model was established by discrete element method (DEM), considering the shape characteristic of muck. The whole muck removal process was simulated, then the influence of the advancement speed and rotational speed on muck removal performance in tuff and granite stratum was studied via numerical simulations. Based on simulation results, the muck removal performance evaluation system of TBM is built using fuzzy mathematics and evaluation theory. Ultimately, optimal operation parameters in the tunnel project is obtained after comprehensive evaluation. The results indicated that the optimum advancement speed should be 7 r/min in both tuff and granite stratum, while the optimal rotational speed was 6 r/min in granite and 5.5 r/min in tuff respectively. Based on TBM engineering application, the size characteristic of muck was obtained from on-site muck specimen analysis and the muck removal performance of TBM under different operation and rock conditions was compared to validate the simulation method. These findings could provide guidance for TBM operation to improve muck removal performance in different geological conditions.