Previous studies showed that the stable β‐form of molecular compound (MC) crystals having a double‐chain‐length structure is formed in a binary mixture system of 1,3‐dioleoyl‐2‐palmitoyl‐sn‐glycerol (OPO) and 1,3‐dipalmitoyl‐2‐oleoyl‐sn‐glycerol (POP) with a 1:1 concentration ratio of OPO and POP. The use of MC crystals made of POP and OPO for edible applications, such as margarine, is advantageous due to no‐trans, low‐saturated, and high‐oleic fats. Industrial manufacturing technology involves rapid cooling processes, and the kinetic properties of crystallization of MC of OPO and POP are required. In this study, we clarified the crystallization of MC of OPO and POP under rapid cooling at rates of 1–150 °C min−1, using synchrotron radiation time‐resolved X‐ray diffraction and differential scanning calorimetry methods. The main results are as follows: (1) POP and OPO crystallized in separate manners without the formation of MC crystals under rapid cooling (>40 °C min−1), while MC crystals started to form with decreasing rates of cooling in addition to the POP and OPO crystals (<30 °C min−1); (2) metastable and stable forms sub‐α, α, β′, and β of POP and OPO were formed, whereas the MC crystals of β were formed during the cooling processes; and (3) the heating processes after crystallization by rapid cooling caused separate melting of the metastable and stable forms of POP and OPO crystals and the formation of MC crystals of β made of POP and OPO, as well as melting of the MC crystals alone.