Abstract: Some side reactions in the synthetic processes of prothioconazole led to by-products. They negatively affect the yield and quality of prothioconazole. Three different synthetic processes were investigated. Four by-products, including 2-(1-chlorocyclopropyl)-1-(2-chlorophenyl)-3-(4H-1,2,4-triazol-4-yl)propan-2-ol (7), 6-(2-chlorobenzyl)-6-(1-chlorocyclopropyl)-5,6-dihydro-4H-1,3,4-oxadiazine-4-carbothioamide (8), dimer-prothioconazole (9) and 2-(2-chlorobenzyl)-2-((5-thioxo-4,5-dihydro-1,2,4-triazol-1-yl)methyl)cyclobutanone (10), were synthesized and characterized by ¹H NMR, ¹³C NMR, ESI-MS or X-Ray diffraction. Among them, the by-product 8 was first discovered during the synthesis of prothioconazole by substituting hydrazine-acetone. The study revealed the mechanism of generation of the four by-products in different processes. The results provided an important guide for the selection and control of the synthetic process of prothioconazole and product quality improvement.