As the existing methods for consistency processing of runoff series were not detailed enough, an improved algorithm for restoring natural runoff in the Yellow River Basin was proposed. The natural surface runoff at the Lijin Station near the Yellow River Estuary was restored and analyzed based on the measured runoff at the station and the data in the basin above the Lijin section, including the surface water consumption, reduction of surface runoff caused by groundwater exploitation, increase of water surface evaporation from artificial reservoirs and check dams, and storage variable of reservoirs. Furthermore, the current natural surface runoff was estimated using the current underlying surface which references the underlying surface during 2001 to 2016. Based on the long series from 1956 to 2016, the natural surface runoff at the Lijin Station of the Yellow River was 57.772 billion m³, and the natural runoff with the current underlying surface was 55.172 billion m³, which was 6.172 billion m³ higher than the results of the third water resources evaluation given by the basin agency.