Microstructures of fullerene derivatives formed via self-assembly strategy facilitate the versatile applications of these zero-dimensional molecules. However, the accurate elucidation of formation mechanism of fullerene microstructures is a challenge issue. A novel fullerene derivative 2 with rigid pyridine substituent was synthesized and characterized by X-ray crystallography. Using the strategy of liquid–liquid interfacial precipitation, self-assembly of 2 affords a micrometer-sized flowerlike and a discoid morphology. Based on the crystal packing of 2, the proper formation mechanism of different morphologies was proposed. Meanwhile, the photoelectrochemical properties of different morphologies of 2 was also unveiled.