Previous studies have shown that the external quantum efficiency (EQE) of conventional red Micro-Light emitting diodes(Micro-LEDs) decreases markedly with reducing chip size. This degradation is generally attributed to enhanced non-radiative recombination at sidewall defects, which leads to increased carrier loss in size-scaled LEDs. In this work, AlGaInP quaternary semiconductor epitaxial wafers incorporating multiple quantum wells (MQWs) with different well-layer strain states were grown by metal–organic chemical vapor deposition (MOCVD). Through wafer bonding, photolithography, etching, and metal evaporation, these epitaxial structures were fabricated into Micro-LED arrays with single-pixel pitches of 10, 20, 50, and 100 μm. The experimental results reveal that, with increasing indium (In) composition in the GaInP well layers—corresponding to a gradual increase in lattice mismatch (Δa/a) from 0% to 1%—smaller-sized Micro-LED arrays exhibit superior EQE performance. For devices with a pixel pitch of 10 μm, the EQE of Micro-LED arrays with a 1% lattice mismatch in the well layer is approximately three times higher than that of lattice-matched (0%) counterparts. In contrast, for devices with a pixel pitch of 100 μm, the EQE of lattice-matched (0%) Micro-LED arrays is about 1.3 times higher than that of devices with a 1% lattice mismatch. These results indicate that, to achieve maximum EQE in Micro-LEDs, the strain state of the MQW-layer material must be carefully considered as a priority factor. Optimal device performance requires appropriate matching between LED size and the well-layer growth strain.