The M-polynomial, introduced by Deutsch and Klavžar in 2015, provides a unifying algebraic framework for the computation of numerous degree-based topological indices such as the Zagreb, Randic, harmonic, and forgotten indices. Despite its broad applications in chemical graph theory and network analysis, closed expressions of the M-polynomial remain unknown for many important graph families. In this work we derive, for the first time, a complete explicit expression of the M-polynomial of the generalized Hanoi graphs $H_p^n$ for arbitrary positive $p$ and $n$. Our derivation relies on a detailed combinatorial analysis of the occupancy-based structure of $H_p^n$, refined using Stirling and $2$-associated Stirling numbers to enumerate all configurations with prescribed singleton and multiton counts. We obtain closed formulas for all diagonal and off-diagonal coefficients of the M-polynomial and show how these expressions yield exact values of the main degree-based topological indices. The correctness of the formulas is supported through numerical computation in small instances. These results provide a complete degree-based description of $H_p^n$ and make their structural complexity fully accessible through the M-polynomial framework.