High-temperature superconducting films can be used for fabricating the cutting-edge high-temperature superconducting microwave devices because of their low microwave surface resistances. However, the microwave surface resistances of high-temperature superconducting materials are particularly sensitive to microstructure due to their special two-dimensional superconducting mechanisms and extremely short superconducting coherence lengths. To investigate the correlations between microstructure and microwave surface resistance of high-temperature superconducting materials, YBa₂Cu₃O_7-δ (YBCO) films with different thickness are grown on (00l)-oriented MgO single-crystal substrates by using the pulsed laser deposition (PLD) technique. Electrical measurements reveal that their superconducting transition temperatures and room temperature resistances do not show significant difference. However, their microwave surface resistances in superconducting state display a significant difference. The characterizations of the microstructures of YBCO films by synchrotron radiation three-dimensional reciprocal space mapping(3D-RSM) technique show that the number of the grains with CuO₂ face parallel to the surface (c crystals), and the consistency of grain orientation are the main causes for the difference in microwave surface resistance.