For the purpose of screening high-efficiency and low-risk green pesticides, a systematic study on fungicide penthiopyrad was conducted at the enantiomeric level. The bioactivity of S-(+)-penthiopyrad (median effective concentration (EC50), 0.035 mg/L) against Rhizoctonia solani was 988 times higher than R-(−)-penthiopyrad (EC50, 34.6 mg/L), which would reduce 75% usage of rac-penthiopyrad under the same efficacy. Furthermore, their antagonistic interaction (toxic unit (TUrac), 2.07) indicated the existence of R-(−)-penthiopyrad would reduce the fungicidal activity of S-(+)-penthiopyrad. AlphaFold2 modeling and molecular docking illustrated that S-(+)-penthiopyrad had the higher binding ability with the target protein than R-(−)-penthiopyrad, showing higher bioactivity. For model organism Danio rerio, S-(+)-penthiopyrad (median lethal concentrations (LC50), 3.02 mg/L) and R-(−)-penthiopyrad (LC50, 4.89 mg/L) were both less toxic than rac-penthiopyrad (LC50, 2.73 mg/L), and the existence of R-(−)-penthiopyrad could synergistically enhance the toxicity of S-(+)-penthiopyrad (TUrac, 0.73), using S-(+)-penthiopyrad would reduce at least 23% toxicity to fish. The enantioselective dissipation and residues of rac-penthiopyrad were tested in three kinds of fruits, and their dissipation half-lives ranged from 1.91 to 23.7 d. S-(+)-penthiopyrad was dissipated preferentially in grapes, which was R-(−)-penthiopyrad in pears. On the 60th d, the residue concentrations of rac-penthiopyrad in grapes were still higher than its maximum residue limit (MRL), but the initial concentrations were lower than their MRL values in watermelons and pears. Thus, more tests in different cultivars of grapes and planting environments should be encouraged. Based on the acute and chronic dietary intake risk assessments, the risks in the three fruits were all acceptable. In conclusion, S-(+)-penthiopyrad is a high-efficiency and low-risk alternative to rac-penthiopyrad.