In the case of the early commissioning phase, the injector system produces electron bunches of 5 MeV with a repetition rate of 1.3 GHz. The compensation of the emittance growth due to the space charge effect was investigated in order to achieve a small emittance at the exit of the merger. We discuss the results of a method to compensate the emittance growth which is based on beam envelope matching between the betatron function and the linear dispersion induced by the space charge force. We investigated the space charge effect when the beam energy in the superconducting RF section was changed. The effect of space charge in the arc section was also investigated. It is shown that the space charge effect in the c-ERL is an important source of distortion of the optics function. In this paper, we show the results on the analysis of the effect of space charge in the compact-ERL at KEK which has a low-energy beam.