  The recently discovered kagome materials $A$V$_3$Sb$_5$ ($A$ = K, Rb, Cs)
attract intense research interest in intertwined topology, superconductivity,
and charge density waves (CDW). Although the in-plane $2\times2$ CDW is well
studied, its out-of-plane structural correlation with the Fermi surface
properties is less understood. In this work, we advance the theoretical
description of quantum oscillations and investigate the Fermi surface
properties in the three-dimensional CDW phase of CsV$_3$Sb$_5$. We derived
Fermi-energy-resolved and layer-resolved quantum orbits that agree
quantitatively with recent experiments in the fundamental frequency, cyclotron
mass, and topology. We reveal a complex Dirac nodal network that would lead to
a $\pi$ Berry phase of a quantum orbit in the spinless case. However, the phase
shift of topological quantum orbits is contributed by the orbital moment and
Zeeman effect besides the Berry phase in the presence of spin-orbital coupling
(SOC). Therefore, we can observe topological quantum orbits with a $\pi$ phase
shift in otherwise trivial orbits without SOC, contrary to common perception.
Our work reveals the rich topological nature of kagome materials and paves a
path to resolve different topological origins of quantum orbits.
