Abstract Background: Variations in phenotypic traits of various plants living in either normal or stressed environments have been well studied, but ecological responses of plants to long-term persistent toxic metal pollution have little been reported. In this study, in order to explore the effects of continuous metal pollution in soil on variation and differentiation in the plants, Rumex crispus L. populations exposed to different levels of long-term persistent toxic metal pollution were studied, and corresponding R. crispus populations that had not been exposed to pollution were used as controls. Results: Six phenotypic traits of R. crispus—root diameter, leaf area, leaf length, leaf width, leaf perimeter, and leaf length-to-width ratio—differed significantly among and within populations. Traits ranked in descending order of coefficient of variation were leaf area, leaf perimeter, root diameter, leaf length, leaf width, leaf length-to-width ratio. The average coefficient of variation was 46%. Phenotypic variation in R. crispus was much greater among populations (92.69%) than within populations (6.55%). The mean phenotypic differentiation coefficient (Vst) of 93.37% indicates that the interpopulation variability was the main source of phenotypic variation in R. crispus. Finally, root diameter was significantly positively correlated with metal factors, but leaf area, leaf length, and leaf aspect ratio were significantly negatively correlated with Pb, Zn, Mn, and Fe contents. Overall, underground growth is superior to aboveground growth in populations that have experienced long-term exposure to toxic metal pollution, and there were phenotypic differences between uncontaminated and contaminated populations. Conclusions: These results indicate that R. crispus adapts to the heterogeneous environment caused by toxic metal pollution through rich phenotypic variation, and ecological differentiation has occurred among different populations.