Magnetotelluric (MT) method is an electromagnetic geophysical method for inferring the earth's subsurface electrical conductivity from measurements of natural geomagnetic and geoelectric field variation at the earth's surface. MT method is widely used in exploration surveys worldwide, but it was hardly applicable in urban areas because of large artificial electromagnetic noise. But in one day, there are several hours at midnight that most of the electric equipment is shutdown. The MT time-series data at midnight is much quiet than in the daytime. Therefore, we focused on calculating the MT impedance using the quiet time-series data. In this research, the data observed by the Phoenix System is used. We introduced a robust impedance estimator based on the Hilbert-Huang transform (RMHHT) and used a new strategy to calculate the broadband MT time-series data. We indicated that this technique needs 4-hour time-series data to get a reliable resistivity structure up to 1,000 seconds in the numerical simulation. This short measurement time makes it possible to carry out MT surveys in urban areas with strong noises. However, the biggest problem of the impedance estimator based on HHT is time-consuming. The total computation time can be reduced significantly by using this strategy. Finally, a successful case study using the midnight time-series data was demonstrated to get reliable resistivity structures in the areas contaminated by heavy noises.