In the present work, we will study the effect that the surface roughness of the sample has on the magnetic and thermodynamic properties in a mesoscopic superconducting meso-square under an external magnetic field in a zero-field cooling process.We will analyze the magnetization, superconducting electronic density, free Gibbs energy, specific heat and entropy as a function of the roughness of the sample in a superconducting two-band square taking a Josephson type inter-band coupling. We show that the magnetic and thermodynamic properties depend on the roughness percentage of its surface. Our investigation was carried out by numerically solving the two-band time-dependent Ginzburg-Landau equations.