This paper presents an analysis on the initial ignoring time of SCW type GHX using Mean Square Error method. Line source method is a useful method for estimating the ground thermal conductivity for the vertical type and SCW type GHX in Korea. The line source method for ground thermal conductivity of geothermal in-site test is the basis of linear approximation between the temperature of a borehole and logarithmic time in a GHX. To apply the line source method to the estimation of SCW type GHX, it is necessary to ignore the initial time of data at the stage of a linear approximation. This paper proposed a new initial ignoring time of SCW type GHX among various initial ignoring time at the time for reaching MSE of $0.02^{circ}C^2$.