We elucidate here the significant effect of non-recrystallization zone reduction on microstructure and mechanical properties in multi-phase steel from the perspective of crystallographic structure, particularly, digitization and visualization of variant pairing. The volume fraction of deformation induced ferrite increased with the increase of non-recrystallization zone reduction, accompanied by the increase of acicular ferrite. This behavior is related to suppression of upper bainite by occupying the prior austenite grain boundaries by allotriomorphic ferrite. The increase of non-recrystallization zone reduction led to a transition from upper bainite to acicular ferrite, and consequently influenced the mechanical properties. The multi-phase steel with a microstructure consisting of ultra-fine ferrite, bainite and a large volume fraction of acicular ferrite had an excellent combination of high yield strength (561 MPa), low yield-to-tensile ratio (0.81), high uniform elongation (11.4%) and remarkable cryogenic toughness of 212 J tested at −100 °C. There was a dominance of V1/V8 pairing in upper bainite, resulting in low density of high angle grain boundaries (HAGBs). While the density of HAGBs in acicular ferrite/bainite was significantly higher because of microstructure refinement by acicular ferrite and the transition in variant pairing from V1/V8 to V1/V2. The V1/V2 pair was primarily related to the boundaries between acicular ferrite and bainite. Moreover, the brittle crack propagated straightly in upper bainite. In contrast, the high density of HAGBs in acicular ferrite/bainite impeded and arrested microcracks before they grew to a critical Griffith crack length, and subsequently suppressed the initiation of cleavage crack and decreased the ductile–brittle transition temperature.