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Objective We aimed to analyze the correlation between radiomic features of pulmonary invasive mucinous adenocarcinoma (PIMA), abnormal expression of the FoxM1 and Sox9 genes, and pathological characteristics of the tumor. Methods From June 2021 to October 2024, we selected 150 patients with PIMA and 150 patients without PIMA from Ningbo No.2 Hospital. CT radiomic parameters and the serum mRNA levels of FoxM1 and Sox9 were compared between the groups and correlated with pathological features. Results Patients with PIMA exhibited higher Kurtosis and Entropy in CT radiomic features and increased mRNA levels of FoxM1 and Sox9 compared to patients without PIMA (P < 0.05). These parameters were negatively correlated with differentiation degree and positively correlated with TNM staging (P < 0.05). Kurtosis, Entropy, plasma FoxM1 mRNA, and Sox9 mRNA are all influencing factors of PIMA (P < 0.05). The combined AUC for differential diagnosis of PIMA was the highest for Kurtosis, Entropy, plasma FoxM1, and Sox9 mRNA levels. Conclusion CT radiomic parameters and the plasma mRNA levels of FoxM1 and Sox9 among patients with PIMA were closely associated with tumor differentiation and TNM staging, offering invaluable references for the differential diagnosis of PIMA.