Background: Subpleural focal organizing pneumonia (FOP) and primary lung malignancy (PLM) are usually confused. The aim of this study was to explore the value of ultrasound (US) and contrast-enhanced ultrasound (CEUS) in the differential diagnosis of FOP and PLM. Methods: A total of 23 patients (mean age: 64.57 ± 11.86 years) with FOP and 100 (mean age: 66.29 ± 11.05 years) with subpleural lesions diagnosed as PLM, confirmed by pathological diagnosis and clinical follow-up, were retrospectively enrolled. The largest lesion diameter, angle between the lesion border and thoracic wall, air bronchial sign, internal blood supply, blood supply form, and pleural effusion examined using conventional US were retrospectively analyzed. The indicators of CEUS included the arrival time of contrast agent in the lesion, lesion–lung arrival time difference, degree of enhancement, distribution uniformity of contrast medium, presence of non-enhancing region, and arterial filling mode in the lesion. A p < 0.05 was considered statistically significant. Results: Presence of air bronchial sign (odds ratio [OR] = 6.18, p = 0.025), acute angle between the lesion border and thoracic wall (OR = 7.124, p = 0.033), and homogeneous enhancement (OR = 35.26, p = 0.01) showed predictive value for the diagnosis of FOP. According to the results of the logistic regression analysis, the area under the receiver operating curve of the above features combined was 0.960, and the sensitivity and specificity were 95.0% and 82.6%, respectively. Conclusions: US combined with CEUS has the potential to differentiate between FOP and PLM.