With the increasingly severe environmental problems caused by cyanobacteria blooms, more attentions are paid to the microcystins (MCs) pollution. MCs can be brought into the soils by irrigation with the cyanobacterial blooms polluted water. A lot of cyanobacterial blooms had been taken out of lakes in past several years. Some of the collection water was directly inoculated in soil as organic fertilizer. Once toxic cyanobacterial collections are put into soil, MCs will be released and migrate from the surface to the deeper layers of the soil after precipitation penetration. Therefore, there is a possibility that soils near the lakes and reservoirs might be contaminated by MCs that caused a harmful effect on soil ecosystems and terrestrial plants, including food crop plants, which may correspondingly pose a serious threat to human and animal health. In this paper, effects of MCs on the accumulation, growth and development of terrestrial plants are introduced, as well as the MCs contamination to groundwater involved. We summarized the toxic mechanism of MCs and discussed the possibility of the effect of MCs on soil organism. A future orientation on the soil MCs research is also discussed.