This article focuses on numerically studying the eigenstructure behavior of generalized eigenvalue problems (GEPs) arising in three dimensional (3D) source-free Maxwell's equations with magnetoelectric coupling effects which model 3D reciprocal chiral media. It is challenging to solve such a large-scale GEP efficiently. We combine the null-space free method with the inexact shift-invert residual Arnoldi method and MINRES linear solver to solve the GEP with a matrix dimension as large as 5,308,416. The eigenstructure is heavily determined by the chirality parameter γ. We show that all the eigenvalues are real and finite for a small chirality γ. For a critical value γ=γ⁎, the GEP has 2×2 Jordan blocks at infinity eigenvalues. Numerical results demonstrate that when γ increases from γ⁎, the 2×2 Jordan block will first split into a complex conjugate eigenpair, then rapidly collide with the real axis and bifurcate into positive (resonance) and negative eigenvalues with modulus smaller than the other existing positive eigenvalues. The resonance band also exhibits an anticrossing interaction. Moreover, the electric and magnetic fields of the resonance modes are localized inside the structure, with only a slight amount of field leaking into the background (dielectric) material.