The lattice Boltzmann method (LBM) has been increasingly used as a stand-alone CFD solver in various biomechanical applications. This study proposes a new fluid–structure interaction (FSI) co-modeling framework for the hemodynamic-structural analysis of compliant aortic valves. Toward that goal, two commercial software packages are integrated using the lattice Boltzmann (LBM) and finite element (FE) methods. The suitability of the LBM-FE hemodynamic FSI is examined in modeling healthy tricuspid and bicuspid aortic valves (TAV and BAV), respectively. In addition, a multi-scale structural approach that has been employed explicitly recognizes the heterogeneous leaflet tissues and differentiates between the collagen fiber network (CFN) embedded within the elastin matrix of the leaflets. The CFN multi-scale tissue model is inspired by monitoring the distribution of the collagen in 15 porcine leaflets. Different simulations have been examined, and structural stresses and resulting hemodynamics are analyzed. We found that LBM-FE FSI approach can produce good predictions for the flow and structural behaviors of TAV and BAV and correlates well with those reported in the literature. The multi-scale heterogeneous CFN tissue structural model enhances our understanding of the mechanical roles of the CFN and the elastin matrix behaviors. The importance of LBM-FE FSI also emerges in its ability to resolve local hemodynamic and structural behaviors. In particular, the diastolic fluctuating velocity phenomenon near the leaflets is explicitly predicted, providing vital information on the flow transient nature. The full closure of the contacting leaflets in BAV is also demonstrated. Accordingly, good structural kinematics and deformations are captured for the entire cardiac cycle.