We numerically explore the structure of quasi-normal (QN) frequencies of the five-dimensional small and large Kerr-anti de Sitter (Kerr-AdS${}_5$) black hole with equal and unequal rotations. Our investigation also covers low and high Hawking temperatures. We then study the stability of the Kerr-AdS${}_5$ black hole and the structure of highly damped QN modes, which would reflect the thermodynamic property of the Kerr-AdS${}_5$ black hole. We find that the highly damped complex QN frequencies of a nearly maximally spinning Kerr-AdS${}_5$ black hole have the periodic separation of the surface gravity at the horizon in the imaginary part while the real part converges to the superradiant frequency, which may be relevant to the pole structure of the thermal Green's function in the corresponding conformal field theory on the Kerr-AdS${}_5$ boundary. Finally, we discuss a relation between the QN modes of the Kerr-AdS${}_5$ black hole and the Hod's conjecture on the horizon area quantization along with the analysis of the horizon topology of the Kerr-AdS${}_5$ black hole. We show that in general, an ultra-spinning Kerr-AdS${}_5$ black hole, whose spin parameter is infinitesimally close to the AdS curvature radius, has its non-compact horizon, and based on the Hod's conjecture, we argue that the horizon area may be continuous, that is, the unit area of the horizon vanishes in the ultra-spinning regime.