This case-control study tested a crisis awareness-based chain warning management model for patients with difficulties cooperating with magnetic resonance imaging (MRI) examinations. All participants experienced difficulties cooperating with MRI examinations and underwent cranial magnetic resonance spectroscopy (MRS) and MRI at the same hospital in China. The control group (n = 1233) underwent examinations from January to June 2023 and received routine nursing care (pre-examination safety notification, instructions on cooperating during the examination, post-examination observation). A crisis awareness chain warning management model was implemented for the intervention group (n = 1352), who underwent examinations from July to December 2023. The groups were compared on average time for examination completion, quality of care and occurrence of complications. Data were collected using a self-devised data collection form. The average length of time to complete MRS and MRI was shorter for intervention group patients than for control group patients. The intervention group showed better pre-examination preparation, examination success rate, image quality attainment rate, and one-time examination success rate, and lower incidence of examination-related complications. This management model could increase MRI examination efficiency, improve quality of care, reduce complications and increase nurses' understanding of nursing continuity and crisis awareness.