Strobilurin fungicides (SFs), a class of new fungicides, use strobilurin A as a lead compound. However, with excessive production and usage, the SF residues in soil and aquatic ecosystems may lead to environmental pollution. The mechanism of action (MOA) of SFs is respiratory inhibition of fungal mitochondria. Specifically, azoxystrobin (AZO), pyraclostrobin (PYR), trifloxystrobin (TRI), fluoxastrobin (FLUO), picoxystrobin (PICO), and kresoxim-methyl (KRE) are considered the most widely used SFs. The toxicities of those six fungicides in the environment are still unclear. The present review summarized the toxicities of the six SFs to terrestrial and aquatic biota, including mice, amphibians, aquatic organisms (fish, daphnia, algae, etc.), apoidea, soil animals (earthworms and Folsomia fimetaria), and soil microorganisms. We also review the residue, fate, and transportation of SFs. The results indicate that SFs are highly toxic to aquatic and soil organisms and pose potential risks to ecosystems. Current toxicology studies are more focused on acute or chronic toxicity, but the underlying mechanisms are still unclear and require further analysis. In addition, a simple and scientific analysis method is needed to compare the toxicity differences of different SFs to the same test organisms or differences in the same SFs to different test organisms.