The vertical phase separation in conjugated polymer-elastomer blend systems plays a critical role in inducing desired film morphology of interconnected polymer nanofibrils for high-performance stretchable electronics. However, the precise control of vertical component distribution remains a great challenge due to the complex interactions among solutes, solvent and substrate in the blend system. Herein, we proposed a strategy to enhance the enrichment of polymer at film surfaces in the conjugated polymer-elastomer blend via increasing polymer molecular weight and systematically investigated the microstructural transition of blends under strain. For this purpose, a number of N2200 polymers with the number-average molecular weight (Mn) below (28, 57, 96 kDa) and above (143 kDa) the critical molecular weight (Mc) were used to blend with SEBS. With the increase of Mn, the phase separation between N2200 and SEBS along depth direction occurred at a greater extent due to the reduced polymer solubility and miscibility of the two components. Film-depth-dependent light absorption spectroscopy (FLAS) measurement shows that the content of N2200 concentrated at the film surfaces is dramatically increased from 66% to 85% as the Mn increases from 28 to 143 kDa, leading to the change of morphology from isolated aggregates to continuous and entangled nanofibril network within SEBS matrix. Under deformation, these nanofibrils formed in the 143 kDa blend film are able to maintain sufficient connections and the crystallites are seldom destroyed, thus guarantee efficient charge transport channels. The mobility of the 143 kDa blend film is 0.188 cm2 V−1 s−1, much higher than that of 28 kDa blend film (0.043 cm2 V−1 s−1) and does not decrease during stretching up to 150% strain.