Abstract: Cyanobacterial blooms worldwide pose severe threat to aquatic ecosystem functions and even human health. Due to environmental-friendliness and high selectivity, allelochemicals have put forward a promising option for inhibiting cyanobacterial overgrowth and therefore mitigating blooms in a short term. This study overviewed the algicidal effects of four types of allelochemicals, i.e., polyphenolics, nitrogen-containing compounds, fatty acids/esters and terpenoids, as well as underlying mechanisms and specific target sites against cyanobacteria, and further evaluated the application potential based on economic costs of highly effective cyanobacterium-inhibiting allelochemicals. The results demonstrated distinctive algicidal characteristics among each type of allelochemicals: Fatty acids/esters were the most cost-effective in algicidal activity, which induced extremely strong toxicity to cyanobacteria at low doses due to various action targets and suppressed target cyanobacterial growth by 50% in concentration range of 0.015—52.95 mg/L; Polyphenolics as the most abundant allelochemicals generally exhibited high algicidal activity with median effect concentration (EC₅₀) ranging from 0.05 to 162.53 mg/L, and could restrain cyanobacterial growth by multiple mechanisms such as inhibiting photosynthesis, disrupting cellular oxidative stress balance and damaging cell wall/membrane structure. However, the theoretical costs vastly differed among highly effective algicidal polyphenolics, whose cost-efficiencies were inferior to fatty acids and thus ranked as 2nd place following fatty acids; N-containing compounds generally exhibited specific and evenly effective algicidal effect against cyanobacterial growth, with EC₅₀ varying from 0.3 to 8.14 mg/L, and induced irreversible cell damage by mainly disrupting cyanobacterial photosynthesis, blocking electron transfer, and destroying cellular structures (including ultrastructure). However, N-containing compounds involved high costs and lowest effectiveness that hindered their wide application. Terpenoids exhibited relatively weak algicidal effect as compared to other three types of allelochemicals, which exerted algicidal effect through multi-routes to mainly disrupt photosynthetic function of cyanobacterial cells, with higher EC₅₀ reaching up to 25.3—228 mg/L that limited their actual application. Consequently, this review summarized joint action effect modes and characteristics of same type and different types of allelochemicals on cyanobacterial (mainly Microcystis aeruginosa) growth to decrease applying dosages of allelochemicals, diminish economic costs and achieve more efficient algicidal effects, and pointed out that allelochemicals number in mixture, action target sites, each allelochemical proportion in mixture and mixture dosage were key factors to determine joint action effect of mixed allelochemicals. This review also proposed that different allelochemicals with diverse and complementary action target sites (referred as ‘multi-target mixture’) could exert synergistic effects, and that proportions of allelochemicals with high algicidal activity should be increased in mixture (referred as ‘new-barrel effect’ synergistic effect). Moreover, this review also proposed that multiple allelochemicals were more likely to arouse synergistic algicidal effects when they were mixed based on their inherent types, contents and proportions actually excreted by plants, which provided novel insights for scientific, comprehensive and reasonable choice, application and optimally mixing of allelochemicals, in controlling cyanobacterial blooms.