A molecular packing model of poly(3-hexylthiophene)-block-peracetylated maltopheptaose (P3HT-b-AcMal7) was proposed based on the X-ray and electron diffraction measurements. The P3HT and AcMal7 segments are confined in the lamellae in which the AcMal7 segments are aligned side by-side. The extended P3HT chain segments are tilted with respect to the lamellar plane and strongly π-stacked. This molecular arrangement results from a subtle balance between segregation strength of the P3HT and AcMal7 blocks, strong π–π interactions of the P3HT backbones, geometrical mismatch between two blocks, space filling requirement, and entropic penalties. The small-angle X-ray scattering (SAXS) analysis above the melting temperature of P3HT block indicates strong segregation strength between P3HT and AcMal7 blocks. Differential scanning calorimetry (DSC), Fourier-transform infrared (FT-IR) spectroscopy, and SAXS measurements underline the improved thermal stability of P3HT crystalline domains in the phase-separated P3HT-b-AcMal7.