Covalent organic frameworks (COFs) have been attracting intense research due to their permanent porosity, designable architecture, and high stability. However, COFs are challenging to crystallize and their synthesis often results in tiny crystal sizes and low crystallinities, which hinders an unambiguous structure determination. Herein, we demonstrate that the structure of low-crystallinity COF Py-1P nanocrystals can be solved by coupling three-dimensional electron diffraction (3DED) with simulated annealing (SA). The resulting model is comparable to that obtained from high-crystallinity samples by dual-space method. Moreover, for low-resolution 3DED data, the model obtained by SA shows a better framework than those provided by classic direct method, dual-space method, and charge flipping. We further simulate data with different resolutions to understand the reliability of SA under different crystal quality conditions. The successful determination of Py-1P structure by SA compared to other methods provides new knowledge for using 3DED to analyze low-crystallinity and nanosized materials.