Heavy metal contamination presents a profound threat to terrestrial biodiversity, yet the genetic adaptation and evolution of field organisms under persistent stress are poorly understood. In this study, the Cd-resistant earthworms Metaphire californica collected from the control (Meihua, MHC) and elevated-pollution (Lupu, LPC) pairwise sites were used to elucidate the underlying genetic mechanism. A 48-h acute test showed that LPC worms exhibited 2.34 times higher LC50 (50% lethal concentration values) compared to MHC ones. The Cd bioaccumulation, metallothionein (MT) protein contents, and MT gene expression of LPC M.californica were all significantly higher than those of MHC worms. The well-known MT gene of M.californica was successfully cloned and identified, however, the encoding nucleotide and amino acids displayed non-observable mutations and the phylogenetic tree also revealed that different populations clustered together. Additionally, the results of transcriptomics sequencing demonstrated 173 differentially expressed genes between LPC and MHC worms, primarily involved in stress-response and detoxification pathways, including signal transduction, material metabolism, and protein exports. The above results confirmed that the crucial MT gene did not undergo genetic mutations but rather exhibited global mRNA regulation responsible for the Cd resistance of M.californica. The current study partially disclosed the stress adaptation and evolution of organisms under long-term in situ contamination, which provides insights into maintaining biodiversity under adverse environment.