High-density attachment of Limnoperna fortunei (LF) would lead to the increase of flow resistance, which has posed big challenges to the normal operation of water conveyance projects. It is very necessary to quantify the flow resistance caused by the attachment of LF. In this study, a 3D geometric model of LF was generated based on real images. Attachment models of LF were generated with different densities and mussel size distributions, whose geometric characteristics were evaluated by some fundamental physical quantities, including attachment thickness, bed coverage, surface vertical roughness, and roughness concentration. Furtherly, a 3D numerical model with specific boundary conditions was established in OpenFOAM to simulate the flow over the LF attachment. Body-fitted mesh was generated using snappyHexMesh based on the LF attachment model. The results show that in high-density scenarios, a big wake zone formed inside LF attachment by the combined effects of each individual LF. Turbulence kinetic energy distribution indicated that LF attachment would cause viscous dissipation thus leading to more energy loss. The flow structure inside LF attachment was controlled by the size and spacing between each individual LF. Manning’s n values were calculated based on the CFD results at different densities. The results show that the flow resistance of LF attachment also followed the classic flow regimes, where in the skimming flow regime, the mussel size distribution played a non-negligible role. Higher flow speed resulted in larger flow resistance, and n could increase more than 90% compared to the scenario without LF attachment.