We would like to improve detection sensitivity by making photoelectron transmission window (SiNx membrane) of liquid cell ultra-thin for liquid measurement using XPS or X-ray PEEM at UHV. In this study, thinning of the membrane using gas cluster ion beams (GCIB) was demonstrated and the burst pressure was compared with those thinned with atomic 400 eV Ar+ ions. It was shown that SiNx membranes thinned by GCIB was 2.5 times higher burst pressure than the Ar+ ions. In addition, improvement of sensitivity of characteristic X-ray from liquid-water induced by low-energy electrons was investigated. By using 4.5 nm thick SiNx membrane etched by GCIB, the X-ray intensity became 1.6 times higher than those from 11 nm thick pristine membrane at electron beam energy of 1.5 keV. This result showed good agreement with Monte Carlo simulation results of the electron-beam-induced X-ray emission from liquid-water beneath SiNx membrane.