Bilayer graphene is a nanomaterial that allows for well-defined, separated quantum states to be defined by electrostatic gating and, therefore, provides an attractive platform to construct tunable quantum dots. When a magnetic field perpendicular to the graphene layers is applied, the graphene valley degeneracy is lifted, and splitting of the energy levels of the dot is observed. Although bilayer graphene quantum dots have recently been realized in experiments, it is critically important to devise robust methods that can identify the observed quantum states from accessible measurement data. Here, we develop an efficient algorithm for extracting the model parameters needed to characterize the states of a bilayer graphene quantum dot. Specifically, we put forward a Hamiltonian-guided random search method and demonstrate robust identification of quantum states on both simulated and experimental data.