Abstract Determining marsquake magnitudes is essential for assessing seismic activity on Mars, yet previous estimates neglect three‐dimensional (3D) scattering effects. The exceptionally long‐lasting coda of the largest recorded marsquake, S1222a, provides a unique opportunity to quantify how crustal heterogeneities affect waveform propagation and magnitude estimation. Here, we perform full 3D waveform simulations for S1222a, incorporating surface topography, lateral crustal thickness variations, and heterogeneous random media. By fitting waveform envelopes in the 0.04–0.08 Hz frequency band, crustal heterogeneities with 20–50 km correlation lengths and 30%–40% maximum velocity perturbations are required to reproduce the observed long‐period scattered surface waves. Accounting for these 3D scattering effects increases the estimated moment magnitude of S1222a to 4.7–4.9, higher than one‐dimensional (1D) estimates and consistent with normal mode observations. Our results demonstrate that neglecting 3D scattering can systematically underestimate marsquake magnitudes by 0.2–0.3, biasing estimates of seismic energy release on Mars.