In this study, an efficient interface, based on a fractionized sampling and stacking (FSS) strategy, was developed for online heart-cutting two-dimensional liquid chromatography (2D LC). This interface consisted of a two-position 4-port valve, a two-position 6-port valve and a two-position 10-port valve equipped with two 450-μL stainless steel loops. Hydrophilic interaction chromatography (HILIC) and reversed phase liquid chromatography (RP LC) were used in the first and second dimensions, respectively. The peak compression efficiency of this interface was investigated by analysis of ten standards. Good peak shapes of the ten standards were observed when the dilution ratio was over five and the co-eluate plug volume was less than 10μL. The 2D LC system was further applied to analysis of a crude extract of Panax ginseng leaves. Seventeen major constituents in the extract were monitored, which could not be well separated by one-dimensional (1D) HILIC or RP LC method in a long separation gradient. The FSS interface successfully achieved the efficient combination of HILIC and RP LC, and the 17 constituents in ginseng extract got well separated under the optimized conditions. The FSS interface has shown great potential for 2D LC analysis of complex natural product samples.