It is well known that a solid surface will be charged when it comes into contact with liquid, especially with electrolyte solutions. The surface charge influences ion distribution and transport and, therefore, affects the chemical reaction. Such an effect may become significant in micropores/nanopores when the electrical double layer thickness is comparable to the pore size, but this has never been well studied. This work investigates the coupled electrokinetic and reactive transport in micropores using mesoscopic modeling. We established a numerical framework by coupling multiple lattice Boltzmann models to combine all effects on ion transport from convection, diffusion and electrokinetics, and therefore, on heterogeneous reactions in micropore. After validations, the mechanism of surface charge effects on reactive transport is studied for an ion precipitation case and a solid dissolution case. The results show that two factors, transport and reaction, compete in such complicated processes based on their characteristic rates. When the transport rate, including diffusion and convection, is much lower than the reaction rate, i.e., the transport-dominated process, the surface charge significantly reduces the reaction. Otherwise for a reaction-dominated process, the surface charge effect may be negligible.