Extensive morphoea causes major morbidity, disability and disfigurement; pathophysiology is poorly understood. The aim of this study was to investigate, with non-invasive imaging, the relationship between localised abnormalities of skin structure and perfusion, which characterise morphoea. Thirty-two patients with morphoea underwent imaging at affected and unaffected sites. Skin thickness was imaged with optical coherence tomography (OCT) and high-frequency ultrasound (HFUS). Perfusion was imaged with dual-wavelength laser Doppler imaging (LDI) and thermography. Epidermal thickness showed a small increase from affected to unaffected site (OCT, active and inactive plaques [p = 0.005 and p = 0.004], HFUS active plaques only [p = 0.03]). Deeper perfusion was higher within affected than unaffected sites (LDI p < 0.001, thermography p < 0.0001, active and inactive plaques). Epidermal thickness was inversely related to superficial (but not deeper) perfusion. This novel study of OCT, HFUS, LDI and thermography confirms loss of epidermal thickness and increased deeper perfusion in morphea plaques.