To investigate the molecular and physiological mechanisms associated with resistance diversity of different pineapple varieties, we utilized the two cultivars, PZ2 and PZ3 with differential stressresistance in this work to comparatively analyze the transcriptome and metabolome. (1) The transcriptome sequencing results showed that a total of 1 667 differential expressed genes were detected in PZ2 and PZ3 comparison group. In PZ3, 770 and 897 differential expressed genes were found to be up and downregulated when compared with PZ2, respectively, and 20 differential expressed genes were involved in adversity resistance, including ASR3, SOD1, POD48, HSP20, GSTF1, GSTU17, as well as WRKY and MYB transcription factor genes. (2) Metabolomics analysis indicated that a total of 208 differential metabolites were identified in PZ2 and PZ3 comparison group, 98 and 110 of those were upand downregulated in contents in PZ3 when compared with PZ2, respectively. Totally, 22 differential metabolites were found to be associated with adversity resistance, including amino acids and derivatives, lipids, flavanols, carbohydrates and glycosides. (3) It showed that the expression profiles of the eight genes revealed by qPCR were consistent with the corresponding RPKM values derived from RNAseq. (4) The correlation analysis showed that the pathways for coenrichment of differentially expressed genes and differential metabolites included flavonoid biosynthesis, phenylpropanoid biosynthesis, tropane, piperidine and pyridine alkaloid biosynthesis, and cysteine and methionine metabolism. It was found that the expression levels of abiotic stress responsive genes, antioxidant enzyme genes, as well as structure and regulatory genes response to stress, were higher in the pineapple cultivar with strong stress resistance than those of the cultivar with stresspoor resistance. Also, the contents of flavonoids, amino acids and derivatives, as well as lignans and lipids metabolites were higher than those of cultivar with stresspoor resistance. The data of this work would contribute to provide references for the comparative analysis of mechanism of pineapple varieties related to different resistance and to provide a theoretical basis for pineapple resistance breeding.