Summary: Precisely predicting laminar-turbulence transition locations is essential for improvements in hypersonic vehicle design related to flow control and heat protection. Currently state-of-the-art \(e^N\) prediction method requires the evaluation of discrete normal modes F and S for the growth rate of instability wave. Meanwhile, in receptivity studies, both the discrete and continuous modes, including acoustic, entropy, and vorticity modes, contribute to the generation of the initial disturbance. The purpose of this paper is to introduce a new very high-order numerical method to accurately compute these normal modes with finite-difference on a non-uniform grid. Currently, numerical methods to obtain these normal modes include two major approaches, the boundary value problem approach and the initial value problem approach. The boundary value approach used by M. R. Malik [J. Comput. Phys. 86, No. 2, 376–413 (1990; Zbl 0682.76043)] deploys fourth-order finite difference and spectral collocation methods to solve a boundary value problem for linear stability theory (LST). Nonetheless, Malik’s presentation only demonstrated the computation of discrete modes, but not the continuous modes essential for conducting modal analysis on receptivity data. To obtain the continuous spectrum for his multimode decomposition framework, A. Tumin [J. Fluid Mech. 586, 295–322 (2007; Zbl 1119.76051)] relies on an initial value approach based on the Runge Kutta scheme with the Gram-Schmidt orthonormalization. However, the initial value approach is a local method that does not give a global evaluation of the eigenvalue spectra of discrete modes. Furthermore, Gram-Schmidt orthonormalization, which can be error-prone in implementation, is required at every step of the integration to minimize the accumulation of numerical errors. To overcome the drawbacks of these two approaches, this paper improves the boundary value approach by introducing a new general very high-order finite difference method for both discrete and continuous modes eigenfunctions. This general high-order finite difference method is based on a non-uniform grid method proposed by X. Zhong and M. Tatineni [J. Comput. Phys. 190, No. 2, 419–458 (2003; Zbl 1076.76564)]. Under the finite difference framework, discrete and continuous modes can be obtained by imposing proper freestream asymptotic boundary conditions based on the freestream fundamental solution behavior. This asymptotic boundary condition is used for obtaining both discrete and continuous modes that have both distinct (acoustic) and similar (vorticity and entropy) eigenvalues. Extensive verification of the new method has been carried out by comparing the computed discrete and continuous modes. Subsequently, the discrete and continuous modes obtained with this finite difference method are essential for the bi-orthogonal decomposition, which holds promising potential in obtaining an accurate evaluation of receptivity coefficients. The result of the bi-orthogonal decomposition for a hypersonic boundary layer flow over a flat plate is verified by comparing with existing results. Ultimately, the bi-orthogonal decomposition using the eigenfunctions has been applied to a case of freestream receptivity simulation for an axis-symmetric hypersonic flow over a blunt nose cone with modal contributions computed as coefficients for receptivity analysis.