This paper investigates the modal behaviors of a deep beam with a transverse open crack. Unlike cracked shallow beams with aspect ratio (L/h) > 10, cracked deep beams with aspect ratio < 5 simultaneously exhibit near the crack both axial-bending coupling mode caused by mode I crack and shear (or sliding) mode caused by mode II crack, referred to as axial-bending-shear modal coupling. Therefore, for accurate modal behaviors prediction, appropriate compatibility equations accounting for both modes I and II crack should be employed for deriving a frequency equation. Because the derived frequency equation is nonlinear with respect to modal frequency, the modal frequencies are calculated through the Newton–Raphson method. The corresponding mode shapes are determined by substituting the calculated modal frequencies into the spectral solutions for either side of the crack. The validity of the proposed method was demonstrated through comparison to the finite element analysis and experimental results.