The widespread of patulin (PAT) and its potential hazards to human health call for alternative rapid assays to monitor it in food and the environment. Herein, we prepared chromium hydroxide [Cr(OH)₃] nanoparticles via a one-pot chemical precipitation strategy and used them to fabricate a turn-on fluorescent aptasensor employing a morphological effect for sensitive PAT detection. Three Cr(OH)₃ nanoparticle structures were synthesized by changing the solvent, and their structures and physicochemical properties were investigated. Then, we evaluated the effects of morphological structures on the fluorescence quenching-recovery capability of Cr(OH)₃ nanoparticles before and after incubation with PAT. We found that the Cr(OH)₃-3 nanoparticles efficiently absorbed the fluorescence dye 6-carboxyfluorescein labeled aptamer (FAM-Apt) and quenched the fluorophore through photoinduced electron transfer. Under optimal experimental conditions, the turn-on fluorescent aptasensor for PAT determination displayed two linear ranges (0.01–10 ng/mL and 1–200 ng/mL) with a low detection limit of 7.3 pg/mL. Moreover, the proposed aptasensor had no cross-reactivity with interferents that usually coexist with PAT and can be used to detect PAT in apple juices accurately. The results of the as-fabricated method were not significantly different from the high-performance liquid chromatography. Hence, we demonstrated that different Cr(OH)₃ nanoparticles can be prepared by changing reaction conditions, and provided a novel strategy to improve the detection performance of fluorescent aptasensor by changing the morphological structure and crystalline properties of nano-quenchers.