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Advancements in the Global Geodetic Observing System (GGOS) have enabled us to investigate the effects of lateral heterogeneities in the internal Earth structure on long-term surface deformations caused by the Glacial Isostatic Adjustment (GIA). Many theories have been developed so far to consider such effects based on analytical and numerical approaches, and 3D viscosity distributions have been inferred. On the other hand, fewer studies have been conducted to assess the effects of lateral heterogeneities on short-term, elastic deformations excited by surface fluids, with 1D laterally homogeneous theories being frequently used. In this paper, we show that a spectral finite-element method is applicable to calculate the elastic deformation of an axisymmetric spherical Earth. We demonstrate the effects of laterally heterogeneous moduli with horizontal scales of several hundred kilometers in the upper mantle on the vertical response to a relatively large-scale surface load. We found that errors due to adopting a 1D Green’s function based on a local structure could amount to 2–3% when estimating the displacement outside the heterogeneity. Moreover, we confirmed that the mode coupling between higher-degree spherical harmonics needs to be considered for simulating smaller-scale heterogeneities, which agreed with results of previous studies.