Amide proton transfer-weighted imaging (APTWI) and multiple models intravoxel incoherent motion (IVIM) based 18F-FDG PET/MR could reflect the microscopic information of the tumor from multiple perspectives. However, its value in the prognostic assessment of non-small cell lung cancer (NSCLC) still needs to be further explored. To determine whether pretreatment APTWI, mono-, bi-, and stretched-exponential model IVIM, and 18F-FDG PET-derived parameters of the primary lesion may be associated with progression-free survival (PFS) in NSCLC. Prospective. Seventy-seven patients (mean age, 62 years, range, 20-81 years) with 37 men and 40 women were included. 3.0 T 18F-FDG PET/MRI, single shot echo planar imaging sequences for IVIM and fast spin-echo sequences with magnetization transfer pulses for APTWI. Patient clinical characteristics (age, sex, smoke, subtype, TNM stage, and surgery), PFS (chest CT every 3 months, median follow-up was 18 months, range, 4-27 months), and APTWI (MTRasym(3.5 ppm)), IVIM (ADCstand, D, D*, f, DDC, and α), and 18F-FDG PET (SUVmax, MTV, and TLG) parameters were recorded. Proportional hazards model, concordance index, calibration curve, decision curve analysis (DCA), and Log-rank test. A P value <0.05 was considered statistically significant. Histological subtype, TNM stage, MTV, D*, and MTRasym(3.5 ppm) were all independent predictors of PFS. A prediction model based on these predictors was developed with a C-index of 0.895 (95% CI: 0.839-0.951), which was significantly superior to each of the above predictors alone (C-index = 0.629, 0.707, 0.692, 0.678, and 0.558, respectively). The calibration curve and DCA indicated good consistency and clinical utility of the prediction model, respectively. Log-rank test results showed a significant difference in PFS between the high- and low-risk groups. APTWI and multiple models IVIM based 18F-FDG PET/MRI can be used for PFS assessment in NSCLC. 3 TECHNICAL EFFICACY: Stage 2.