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Based on our previous work on the structural modification of the lead compound I , three series of novel fluorine-containing phosphonates derivatives ( II, III and IV) were designed and synthesized. Their post-emergence herbicidal activities against some species of weeds were evaluated in a green house. The compounds II were synthesized by introducing of two methylene into the structure I . Compared with the commercial herbicidal clacyfos, compounds II showed moderate herbicidal activity with 60–85% inhibition effect against chingma abutilon ( Abutilon theophrasti ), common amaranth ( Amaranthus retroflexus ) and white eclipta ( Eclipta prostrate ) at a rate of 150 g ai/ha. The compounds III were designed by introducing open-chain phosphonates, which displayed notable herbicidal activity. Especially, the compounds III-1 – III-4 , III - 6 , III - 8 , III - 11 and III - 12 exhibited significant herbicidal activity (80–100%) comparing to the clacyfos against all tested broadleaf weeds, while compounds IV with five carbon atoms in the carboxylic acid chain were inactive against all of the tested weeds. Structure-activity relationship analyses indicated that the length of the carbon chain had a great effect on the herbicidal activity. Furthermore, a broad spectrum test confirmed that compounds III - 4 and III - 8 were comparable with glyphosate against all of the tested weeds at a rate of 75 g ai/ha.