Chain shuttling polymerization enables an efficient production of ethylene octene block copolymers (OBCs) that combine different mechanical properties in a polymer chain. However, this method results in molecular weight polydispersity and multiblock chain structure. The melt-phase behavior and mesophase transition of the polydisperse OBCs with low octene content but different molecular weight and block composition were investigated by rheology, differential scanning calorimetry (DSC), atomic force microscopic (AFM), polarized optical microscopy (POM), and small-angle X-ray scattering (SAXS). Three rheological methods, namely the deviation of the scaling dependence of zero shear viscosity on molecular weight, the terminal behavior and the failure of time temperature superposition (TTS), and two-dimensional rheological correlation spectrum, are used to reveal the mesophase separation with increasing sensitivity. The occurrence of mesophase separation transitions (MST) was observed in such low octene content and low molecular weight OBC systems, with much lower degree of segregation than the theoretical predictions in diblock copolymers. The extent of mesophase separation is further justified by its effect on subsequent crystallization behaviors.