We have improved previously developed compact magnetometer using HTS-SQUID with rotating sample. In the previous system, the attenuation of rotating speed had resulted to the deformation of the averaged waveform signal, reducing the reproducibility in measurements. In this paper, we have used a more superior motor in order to decrease the attenuation of the rotational speed for the precise averaging of the output signal and improving the signal-to-noise ratio. Moreover, to improve sensitivity, we optimized the pickup coil and compared the signal-to-noise ratio of the circular and elliptical pickup coils which having the same number of turns, resistance and inductance. As a result, the signal-to-noise ratio was improved with high accuracy and the magnetometer showed susceptibility sensitivity of 3.8×10-9 emu.