Short-chain chlorinated paraffins (SCCPs) disturb cellular energy metabolism in vitro, but their subcellular toxicity mechanisms are incompletely understood. This study employed mitochondrial metabolomics integrated with phenotypic assays to investigate the subcellular mechanisms of SCCP-induced energy metabolism inhibition. Exposure to SCCPs (0-100 μg/L) caused profound downregulation of ATP. Seahorse respirometry analyses revealed the dose-dependent inhibition of oxidative phosphorylation and compensatory upregulation of glycolysis. Mitochondrial ultrastructural damage (swelling and cristae loss) and dissipation of mitochondrial membrane potential confirmed mitochondria as the primary targets of SCCPs. Mitochondrial metabolomics demonstrated that the suppression of the TCA cycle (depleted citrate, oxaloacetate) and OXPHOS (reduced NAD+, ATP/ADP; inhibited Complex V activity) is responsible for the downregulation of ATP. The conversion from phosphatidylcholines to lysophosphatidylcholines further verified mitochondrial membrane damage. Perturbations in nucleotide metabolism reflected impaired synthesis pathways for DNA/RNA. Critically, medium-chain chlorinated paraffins (MCCPs), proposed as SCCP substitutes, induced qualitatively similar mitochondrial damage (respiration inhibition, cristae disruption, and ΔΨm loss), challenging the presumed safety of MCCPs as alternatives. This study revealed the key mechanisms of SCCP induced energy metabolism inhibition at the subcellular level, underscoring the need for careful reconsideration of MCCP usage.