We report in situ x-ray diffraction (XRD) study of 200 MeV Ag ion irradiation induced structural modification in c-axis oriented YBa2Cu3O7-y (YBCO) thin films at 89 K. The films remained c-axis oriented up to a fluence of 2×1013 ions cm-2, where complete amorphization sets in. The amorphous ion tracks, the strained region around these tracks, and irradiation induced point defects are shown to control the evolution of the structure with ion fluence. Secondary electrons emanating from the ion paths are shown to create point defects in a cylindrical region of 97 nm radius, which corresponds to their maximum range in the YBCO medium. The point defects are created exclusively in the CuO basal planes of fully oxygenated YBCO, which has not been possible, by other techniques including low energy ion irradiation and thermal quenching. The point defects led to a faster decrease in the integral intensity of XRD peaks at very low fluences of irradiation (Φ≤3×1010 ions cm-2) than what can be expected from amorphous tracks. The radius of amorphous ion tracks, estimated from the fluence dependence of integral XRD peak intensity beyond this fluence, was found to be 1.9 nm. Both point defect and the strained region around amorphous ion tracks are shown to contribute to the increase in the c-parameter at 89 K. The full width at half maximum (FWHM) of XRD peaks arising mostly due to the strained region around the ion tracks showed an incubation effect up to 1012 ions cm-2, before increasing at higher fluences. Fluence dependence of FWHM gives the cro- ss section of the strained region as 37.9 nm2, which is more than three times the cross section of the amorphous ion tracks.