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Over the first billion years of Mercury's history, mantle melting and surface volcanism produced a secondary magmatic crust varying spatially in composition and mineralogy. By combining geochemical mapping from MESSENGER with laboratory experiments on partial melting, we translate the surface mineralogy into lateral variations of surface density and calculate the degree of mantle melting required to produce surface rocks. If lateral density variations extend through the whole crust, the local crustal thickness correlates well with the degree of mantle melting. Low-degree mantle melting produced a thin crust below the northern volcanic plains (19 +/- 3 km), whereas high-degree melting produced the thickest crust in the ancient high-Mg region (50 +/- 12 km), refuting the hypothesis of an impact origin for that region. The thickness-melting correlation has also been observed for the oceanic crust on Earth and might be a common feature of secondary crust formation on terrestrial planets.