Samples of sediment and cyanobacteria were collected at a cyanobacteria gathering area of western-half area of Lake Chaohu. The distribution patterns of seven heavy metals (Cd, Cr, Cu, Zn, Pb, Ni and Mn) were studied, and the fractions of Cd and Mn were analyzed using the European Communities Bereau of Reference (BCR) sequential extraction procedure. In addition, laboratorial experiments were carried out to simulate the variations in the heavy metal contents during the cyanobacteria humification, and the effect of cyanobacteria humification on the adsorption and desorption of heavy metals were discussed. The results showed that the heavy metal contents of surface sediments exceed the background values, presenting different values of each sampling site. The closer near the Nanfei River, the higher pollution degree was. Potential Mobile Index analysis showed that, compared to Mn, Cd was more likely to cause the secondary pollution in the western-half area of Lake Chaohu. Correlations analysis indicated that both two heavy metals (Cd and Mn) showed a significant positive correlation between metal speciation and total metal value. Lake Chaohu was considered as a typical algae lake, and the sources and distributions of two heavy metals (Cd and Mn) were related to the algae boom. Combined with the study of adsorption and release by cyanobacteria humification, the present study speculates that the cyanobacteria humification could influence the migration and release of Cd and Mn in Lake Chaohu.