Lab scale and pot experiments were conducted to compare the effects of synthetic chelators and low molecular weight organic acids (LMWOA) on the phytoextraction of multi-contaminated soils by two ecotypes of Sedum alfredii Hance. Through lab scale experiments, the treatment dosage of 5 and 10 mM for synthetic chelators and LMWOA, respectively, and the treatment time of 10 days were selected for pot experiment. In pot experiment, the hyperaccumulating ecotype (HE) was found more tolerant to the metal toxicity compared with the non-hyperaccumulating ecotype (NHE). EDTA for Pb, EDDS for Cu, and DTPA for Cu and Cd were found more effective to enhance heavy metal accumulation in the shoots of S. alfredii Hance. Compared with synthetic chelators, the phytoextraction ability of LMWOA was lesser. Considering the strong post-harvest effects of synthetic chelators, it is suggested that higher dosage of LMWOA could be practiced during phytoextraction, and some additional measures could also be taken to lower the potential environmental risks of synthetic chelators in the future studies.