Quantitatively understanding reactive transport in matrix-fracture systems and the corresponding effect on reservoir fluid flow and heat transfer behavior is essential for the prediction of long-term thermal performance in enhanced geothermal systems (EGSs). However, most previous studies on EGSs only considered fracture reactive transport, overlooking matrix reactive transport and its potential impact on fracture flow and reactive transport. In this study, we develop a thermal-hydraulic-chemical coupled EGS model incorporating both fracture and matrix reactive transport to comprehensively investigate the effect of matrix reactive transport on the long-term thermal performance of the EGS model. We find that matrix reactive transport intensifies exchange fluxes between fracture and matrix, thus weakening water-rock reactions in fracture and suppressing fracture deformation, and ultimately improves thermal performance. The modeling results reveal that fracture aperture increment is overestimated by 67 times and the production lifespan is underestimated by 17 years if matrix reactive transport is ignored. Further dimensionless analyses indicate that the significance of matrix reactive transport increases with reaction rate and declines with porosity/permeability when the Damkohler number (Da) is less than one (reaction-limited). In EGS and karst reservoirs, matrix reactive transport markedly influences heat extraction efficiency, whereas its effect is negligible in sandstone reservoirs in this study.