Variant pairs have an indispensable function on mechanical properties such as low impact toughness. Therefore, it was assumed that they would also affect the HER (Hole Expansion Ratio, an indicator to evaluate stretch flanging performance). To clarify this, a comprehensive analysis of the common influential factors in an 800 MPa grade low carbon micro-alloyed steel, i.e., the retained austenite, the M/A (Martensite/Austenite) island, the titanium precipitations, the grain diameter, the density of high angle grain boundaries and the textures, was first conducted. It was found that they did not match well with the HER, suggesting that they were not the governing factor for HER in this steel. However, the dominating crystallography groups and the variant pairing results indicated that they fitted well with the HER. In the samples with high HERs, the CP (Close Packed) groups dominated the transformation, wherein one individual CP group consisted of two or more Bain groups, whereas it evolved into the domination of joint CP groups and Bain groups for the low HER sample. Further analysis on the variant pairing features indicated that a correlation occurred between the HER and the high angle variant pairs. In the steels with high HERs, high-angle variant pairs of V1/V2, V1/V3 that transformed from the same CP group, particularly of V1/V2 pair, were mostly generated. They turned to V1/V9, V1/V10, V1/V12, V1/V15, V1/V17, and V1/V18 pairs from differential CP groups, especially the V1/V12 and V1/V15 pair for low-HER steel. This result showed that V1/V2, V1/V12, and V1/V15 might have accounted most for the HER in this steel. The underlying reason was that the V1/V2 pair was specialized in supplying a slip passage for dislocation transmission across a grain boundary with little resistance, whereas the dislocation transmission ability for V1/V12 and V1/V15 pair was particularly poor. Thus, to efficiently enhance the HER, one should regulate the variant pairs by augmenting the V1/V2 fraction and suppressing the formation of the V1/V12 and V1/V15 pair.