Purely organic long-persistent luminescence materials (OLPLMs) have received extensive attention in recent years due to their “green” preparation process, environmental friendliness and renewable resource characteristics. As an important branch of OLPLMs research and development, organic crystalline materials exhibit excellent long-persistent luminescence (LPL) properties through a facile crystal fabrication. However, no studies have yet highlighted how to enable flexibility of crystal-based OLPLMs. Here, we utilize a host-guest doping system and water-based preparation under ambient conditions to obtain two organic doped-crystals with different LPL durations due to the minor difference in guest structure. Then, we fabricate high-quality polymer fibers containing these two crystals separately to weave the flexible thin-film by electrospinning, still exhibiting outstanding LPL performance. This work sheds light on the molecular design of host-guest doping system, and will accelerate the research and development of large-area flexible manufacturing of crystal-based OLPLMs.