Hierarchical self-assembly of organic molecules or assemblies is of great importance for organic photonics to move from fundamental research to integrated and practical applications. Magnetic fields with the advantages of high controllability, non-contact manipulation, and instantaneous response have emerged as an elegant way to prepare organic hierarchical nanostructures. In this perspective, we outline the development history of organic photonic materials and highlight the importance of organic hierarchical nanostructures for a wide range of applications, including microlasers, optical displays, information encoding, sensing, and beyond. Then, we will discuss recent advances in magnetically controlled assembly for creating organic hierarchical nanostructures, with a particular focus on their potential for enabling the development of integrated photonic devices with unprecedented functionality and performance. Finally, we present several perspectives on the further development of magnetically controlled assembly strategies from the perspective of performance optimization and functional design of organic integrated photonics.