At Waseda University, we are developing a table-top size soft X-ray source based on inverse Compton scattering between a high quality electron beam and a high power laser. Using 1047 nm laser beam (Nd:YLF) and 4.6 MeV electron beam generated from a photo-cathode rf-gun, we had already succeeded in generating inverse Compton X-rays. The energies are within the “water window” region (250–500 eV) which can be applied to biological studies. For good signal to noise ratio ( S/ N) and a larger number of photons, we remodeled our collision chamber and laser amplifier system. S/ N is defined by the X-ray photon signal over all other noises and backgrounds such as a bremsstrahlung X-rays from a lost electron beam and an electric noises caused by a radiation and rf power source. With these modifications, the X-ray photons detected by a micro channel plate (MCP) have increased 10-fold to reach 312 ph/pulse. Total generated photons were estimated to be 3.3×10 4. Further, we succeeded in generating stable soft X-rays for more than 12 h. Good S/ N ratio, stable X-rays have made it possible to observe the beam–laser interaction very precisely. By using this technique, we have measured the electron beam size at the collision point as 251 μm ( σ x )×56 μm ( σ y ).