Direct observation of organic molecular nanocrystals and their evolution using electron microscopy is extremely challenging, due to their radiation sensitivity and complex structure. In this contribution, we introduce 4D-scanning confocal electron diffraction (4D-SCED), which enables direct in situ observation of the structure and structural evolution in bulk heterojunction (BHJ) thin films. 4D-SCED combines confocal electron optic setup with a pixelated detector to record focused spot-like diffraction patterns with high angular resolution. Thanks to the high signal-to-noise and signal-to-background character, similar data quality can be acquired using an order of magnitude lower dose than previous methods. We apply it to study structure of 2D organic molecular crystals and of active layer in organic solar cells, namely DRCN5T:PC71BM BHJ thin films. Structural details of DRCN5T nano-crystallites oriented both in- and out-of-plane are imaged at ~5 nm resolution and dose budget of ~ 5 e-/Å2. We use in situ annealing to observe the growth of the donor crystals, the evolution of the crystal orientation, and progressive enrichment of PC71BM at interfaces. This highly dose-efficient method opens new possibilities for studying beam-sensitive soft materials.