Superconductivity in flat-band systems, such as twisted bilayer graphene, exhibits unconventional behaviours which cannot be described by the BCS theory. In this work, we derive an effective Lagrangian from a microscopic flat-band Hamiltonian which allows us to establish a Ginzburg-Landau (GL) theory includes the quantum geometric effects in flat-band superconductors. First of all, we deduce the the critical temperature of a flat-band superconductor within the mean field description which is determined by the quantum metric. Secondly, going beyond the mean-field approximation by taking into account the fluctuations of the order parameter, we determine the superfluid weight, superconducting coherent length and the upper critical field and their dependence on the quantum metric of the flat bands. Thirdly, we apply the GL to twisted bilayer graphene (TBG). By calculating the quantum metric of flat bands of TBG, the GL theory allows the estimation of the superconducting coherence length and the upper critical field. The results of the superconducting coherence length and upper critical field match the experimental results incredibly well without the fine tuning of parameters. The GL theory with quantum metric provides a new and general theoretical understanding of unconventional behaviors of flat-band superconductors.