Karst regions are relatively short of arable land, but heavy metals are at high levels in arable land. Under this circumstance, different tillage methods have different effects on the activity of heavy metals in soil. In this study, through field experiments and lab analysis, the effects of different rotation systems on the activity of heavy metals and the transport and enrichment of heavy metals in soil when rape and rice were in different growth stages were analyzed. The results show that in rice-rape rotation, the distribution of the heavy metal content in soil was different. The contents of Cr, Pb and Cu in soil were at the level of “clean” and the content of Cd was at the level of middle pollution. The sequence of the enrichment factors in the growth of the rape was: Cd>Cu>Pb>Cr and its ability to accumulate the same heavy metal varied from different growth stages; leaf, root and stem were main enrichment organs, among which stem had the weakest enrichment ability for Cu, root was the main enrichment organ for Pb and rape had relatively weaker enrichment and transport ability for Cr. Rice mainly accumulated Cd and Cu; it had relatively weaker enrichment ability for heavy meals in the seedling and tillering stages; its enrichment ability for Cd was gradually strengthened; and heavy metals were mainly enriched in rice’s root system in various growth stages.