Bridging the mesoscopic blend structure and property to macroscopic device performance is a key issue for further improvement of photovoltaic conversion efficiency in polymer solar cells (PSCs). The present paper provides a detailed study of the composition and morphology of the blend film of poly(3-hexylthiophene) (P3HT) and [6,6]-phenyl C61-butyric acid methyl ester (PCBM), a classical system in PSC. The electrostatic interactions and charge separation were studied using electrostatic force microscopy and Kelvin probe force microscopy. The correlation was directly constructed between the mesoscopic morphology and the macroscopic device performance (highest efficiency above 4%). The hierarchical phase separation behavior of P3HT in the active layer is beneficial for efficiency improvement. A micro–nano hierarchical phase separation model is proposed to describe the ideal mesoscopic structure of the active layer. This model may also provide a guideline for the rational design of high performance devices with novel materials.