Grey mold, caused by the fungus Botrytis cinerea Pers ex Fr., is one of the most destructive spoilage diseases, severely affecting tomato production in Henan Province, China. Spraying fungicides from the flowering to the harvest stage is a necessary measure to reduce losses associated with B. cinerea infection. However, B. cinerea has developed resistance to fungicides in many countries. Boscalid is a succinate dehydrogenase inhibitor (SDHI) fungicide, and was registered for the control of grey mold. In this study, a total of 269 B. cinerea isolates were collected from tomato in commercial greenhouses in different locations of Henan Province, in 2014 and 2015. The sensitivity and resistance of B. cinerea field isolates were determined based on mycelial growth. The effective concentration 50 (EC50) ranged from 0.11 to 15.92 μg ml−1 and 0.16 to 8.54 μg ml−1, in 2014 and 2015, respectively. The frequency of low resistance to boscalid was 12.6% and 7.6%, and moderate resistance were 2.7% and 1.3%, in 2014 and 2015, respectively. No high-resistant isolates were found in Henan Province, China. Mycelial growth, mycelial dry weight, spore production, and pathogenicity were not significantly different between resistant and sensitive phenotypes of the B. cinerea isolates. The results of cross-resistance test showed no correlation between boscalid and carbendazim, procymidone, pyrimethanil, fluazinam or fluopyram. In this study, the succinate dehydrogenase gene B (sdhB), C (sdhC), and D (sdhD) were analyzed and compared in sensitive, low and moderately resistant B. cinerea isolates to boscalid. Results showed point mutations occurred simultaneously at sdhC amino acid positions 85 (G85A), 93 (I93V), 158 (M158V), and 168 (V168I) in 4 out of 10 sensitive isolates, 23 out of 26 low and 5 out of 5 moderately resistant B. cinerea isolates to boscalid. No point mutations were found in the sdhB and sdhD genes of all isolates. Furthermore, no point mutations were found in sdhB, sdhC and sdhD genes in 3 out of 26 low resistant B. cinerea isolates to boscalid. Therefore, we speculate the simultaneous point mutations in the sdhC gene may not be related to the resistance of B. cinerea to boscalid. These results suggested that there might be a substitution mechanism for the resistance of B. cinerea to the SDHI fungicide boscalid.