Pear anthracnose, caused by Colletotrichum fructicola, is a devastating disease that seriously affects most pear varieties, thereby compromising their yield and quality. However, effective control of this pathogen is lacking. To investigate these resistance mechanisms of pear against C. fructicola, transcriptomic and metabolomic were performed in pear anthracnose-resistant pear variety ‘Seli’ and the susceptible variety ‘Cuiguan’ after infection with C. fructicola, respectively. The differentially expressed genes and differentially accumulated metabolites (DAMs) were mainly related to metabolism and secondary metabolite synthetic pathways, including alpha-linoleic acid and phenylalanine biosynthesis metabolism, unsaturated fatty acids biosynthesis, and amino acids and derivatives biosynthesis etc. In particular, the accumulation of unsaturated fatty acids, amino acids and derivatives, such as linoleic acid and derivatives, lauric acid, N-acetyl-L-glutamic acid and L-proline were significantly increased in ‘Seli’ upon C. fructicola infection, while the amino acids of oxiglutatione and N-acetyl-L-glutamic acid, as well as the proanthocyanidins were significantly decreased in ‘Cuiguan’ upon C. fructicola infection, indicating that these metabolites were responsible for the different levels of resistance to anthracnose in ‘Seli’ and ‘Cuiguan’. Overall, our results provided new insights into pear anthracnose resistance regulation, and this may assist in developing new strategies to control pear anthracnose.