We have been developing a compact X-ray source via laser Compton scattering(LCS) at Laser Undulator Compact X-ray source(LUCX) accelerator in KEK. In here, a multi-bunch electron beam is generated by a 3.6cell photo-cathode RF-gun and accelerated to 18-24MeV by a 12cell accelerating tube. And then 6-10 keV X-rays are generated by LCS between the beam and a laser pulse stored in a 4-mirror planar optical cavity. Presently, we have achieved the generation of 24MeV beam with total charge of 600nC in 1000bunches. The energy difference is within 1.3% peak to peak. The beam-loading is compensated by T method and amplitude modulation of the RF pulse. However, there is the energy difference at the RF-gun. It is assumed that this causes the reduction of the X-ray flux due to change of the focused beam size. To reduce the energy difference, RF amplitude modulation is also applied to the RF pulse for the gun. The results of this beam-loading compensation will be reported.