The interaction between ion beam and solid target is widely used in material modification. For the high temperature superconducting thin film modification, however, earlier experiments show that the samples are accompanied by the degradation in superconducting properties due to the structural damage of materials. In order to improve surface morphologies and superconducting properties of YBa2Cu3O7- (YBCO) thin films, we introduce a new ion beam structure modification (ISM) method. Although the ion bombardment time parameter effect is not clear, the related mechanism should be clarified. In this paper, the bombardment processes with duration times of 8 min, 10 min and 12 min are investigated in a vacuum chamber with an Ar+ Kaufman ion source, and the direction between the incident ion beam and the normal of sample is fixed at a certain angle. Surface morphologies and the microstructures of YBCO samples are characterized by scanning electron micrographs and X-ray diffraction patterns, respectively. In the respect of superconducting properties, the critical current density Jc is measured by Jc-scanning test. The results indicate that the needle-like a-axis grains and pores disappear gradually with the increase of the ion bombardment time. In order to characterize the effects of ion beam bombardment time on the internal strain in YBCO thin films, the relationship between the full width at half maximum and the Bragg diffraction angle of YBCO (00l) peak is studied by the William-Hall equation. The results show that the internal strain in YBCO thin film increases with increasing the ion beam bombardment time. At the same time, the critical current density Jc value of the sample after ISM processing increases, which is more than 2.2 times higher than that of the initial sample. The main reason for the increases of critical current density Jc in YBCO thin film is due to the drastic shrink of CuO bond caused by the increasing internal strain. Based on the bond contraction pair theory, the shrink of CuO bond improves the energy to break Cooper-pairs, and then increases the current carrying capacity of high temperature superconducting YBCO thin film, especially in copper-oxygen (CuO2) plane. The ISM process might be a useful method of markedly improving the surface morphology, meanwhile, the critical current density Jc value also increases in high temperature superconducting YBCO thin film.