123 extended-spectrum β-lactamase-producing Escherichia coli(ESBL-EC) were isolated and collected from food-producing animals(swine and chicken) of different farms in Sichuan province from 2010 to 2016. PCR and DNA sequencing were performed to detection blaCTX-M genes. Pulsed-field gel electrophoresis(PFGE) was used for molecular typing of 33 isolates of the 123 isolates with different sources. The results showed that prevalence of blaCTX-M was 91.9%(113/123) in ESBL-EC isolates, among which blaCTX-M-55 and blaCTX-M-65 were the dominant genotypes. The occurrence of blaCTX-M was increasing yearly; blaCTX-M variants were observed in isolates from chicken and swine; 9 types of mutations of blaCTX-M genes were found in 12 isolates, in which 10 were sense mutations, which made 7 types of amino acid substitutions; 33 isolates were classified into 32 types by PFGE. In sumary, blaCTX-M genotypes were mutated, and had spread widely among different molecular types of ESBL-EC isolates from food animals in Sichuan province.