Background Imatinib (IM) is the primary treatment for Gastrointestinal stromal tumor (GIST), but it faces significant challenges with resistance and a high incidence of adverse events. This study aims to assess the predictive value of baseline body composition parameters on treatment-related adverse events and disease-free survival (DFS) in GIST patients treated with imatinib. Materials and Methods A single-center retrospective analysis was conducted on 107 moderate or high-risk stratification GIST patients diagnosed from 2014 to 2020 at the First Affiliated Hospital of Nanjing Medical University. Body composition parameters, including skeletal muscle index (SMI), myosteatosis, cachexia index (CXI), and Fat-Free Mass (FFM), etc. were obtained using abdominal CT images and clinical data. Logistic and COX regression models were used to analyze the relationship between these indicators and treatment-related adverse events and DFS. Results Multivariate analysis revealed that myosteatosis (OR=7.640, P<0.001) and drug dose (OR=1.349, P=0.010) were independent risk factors for adverse events, while a higher CXI (OR=0.983, P=0.017) was protective. Additionally, LAMA/SMA% (OR=1.072, P=0.028) was identified as an independent risk factor for dose-limiting toxicity (DLT). Independent predictors of DFS included sarcopenia (HR=3.067, P=0.013), myosteatosis (HR=6.985, P=0.024), risk stratification (HR=9.562, high-risk vs. moderate-risk, P=0.003), and C-KIT mutation (HR=3.615, C-KIT exon 9 mutation vs. 11, P=0.013). Conclusions Baseline body composition parameters, particularly myosteatosis, effectively predict the adverse events and DFS in patients taking imatinib. Personalized treatment, such as targeted nutritional and exercise interventions, and close monitoring of patients with myosteatosis or sarcopenia can enhance compliance and improve survival rates.