The general chemical formula of garnet can be expressed as X₃Y₂(ZO₄)₃ where X, Y, and Z represent dodecahedral, octahedral, and tetrahedral sites, respectively. Lithium, phosphorus, and rare earth elements (including yttrium) in garnets from the Luanzhuang-Guanpo and Ziyugou (ZYG) pegmatite fields in the East Qinling orogen and the Kalu’an (KLA) Li pegmatites in the Chinese Altay orogen have been investigated both at a mineral scale and in the context of pegmatite types to identify the substitution mechanisms for these elements. Our results show that Y + REE or P can enter the garnet lattice through coupled substitution with Li (+Na) that can compensate the charge differences due to Y + REE in the X-site or P in the Z-site of the garnet. Two substitutions, namely [^X(Li,Na)⁺₁^X(Y,REE)³⁺₁(R²⁺)_–2] and [^X(Li,Na)₁^ZP₁^XR²⁺_-1^ZSi_-1], are likely the most important and can account for incorporation of the majority of Y + REE, P, and Li + Na in pegmatite garnets. Whichever substitution becomes predominant in garnets is strongly dependent on the bulk chemistry of pegmatite-forming melts. Consequently, the first substitution dominates in garnets from NYF (niobium-yttrium-fluorine) pegmatites and mixed-type pegmatites with NYF affinity whereas the other one dominates in garnets from relatively P-rich LCT (lithium-cesium-tantalum) and barren pegmatites. Incorporation of Sc and Ti in garnet may also need Li + Na, although Sc and Ti are not as much as Y and REE in pegmatite garnet. The zonings of Y, REE, and Sc in garnet are mainly controlled by the composition of pegmatite-forming melt and consumption of these elements due to the growth of garnet itself and other minerals enriched in Y + REE (e.g., xenotime, fergusonite, monazite, etc.) or Sc (e.g., biotite). Additionally, our results, combined with the data in the literature, show that garnets from NYF pegmatites and mixed-type pegmatites with NYF affinity commonly contain elevated Y (up to ∼ 20000 ppm), REE (up to ∼ 20000 ppm), and Sc (up to ∼ 2400 ppm) but low P (<100 ppm) compared to those from LCT and barren pegmatites. Nevertheless, individual garnets with low concentrations of Y, REE, Sc, and P can occur in any types of pegmatites. Therefore, the coupled substitution between Li + Na and Y + REE or P along with zonings and concentrations of Y, REE, and Sc in garnet should be investigated on a regular basis to interpret pegmatite petrogenesis.