Intercritical tempering at 680°C for different times was carried out in a low carbon copper-bearing steel to study the evolution of the crystal structure of Cu precipitates by high resolution transmission electron microscopy. With increased tempering time, four different types of crystal structure of copper precipitates with different sizes were observed, namely, (a) nano-ordered clusters comprised of B2 FeCu nano-ordered clusters (2–3nm) and weak ordered BCC Cu nanoclusters (2–3nm), (b) 9R Cu (5–12nm) - multiple twinned structure consisted of two, six or seven 9R twins with an orientation relationship of (1 1–4)9R∥(0 1 1)α, −1 1 09R∥1 −1 1α, (c) detwinned 9R Cu (24–26nm) consisted of two 9R parts and a removable interface (1 1–4)9R, and (d) FCC Cu (~37nm) precipitates consisted of two parts of FCC Cu and a micro-twinned region. The evolution sequence of crystal structure of Cu precipitates was: nano-ordered clusters→9R Cu→detwinned 9R Cu→FCC Cu. The maximum contribution to precipitation hardening is attributed to nano-ordered clusters. Heat treatment process of experimental steel, hardness data of experimental steel, evolution sequence of crystal structure of Cu precipitation, and schematic of evolution process of Cu precipitation. Display omitted •B2-FeCu nano-ordered clusters exist in the studied steel.•The detwinned process of 9R-Cu has been revealed.•The crystal structure sequence of Cu precipitation with different time of intercritical tempering has been identified.•The maximum contribution to precipitation hardening is attributed to nano-ordered clusters.