Background Postoperative pulmonary embolism (PE) is a serious thrombotic complication in the patients with otolaryngologic cancers. We investigated the risk factors associated with postoperative PE after radical resection of head and neck cancers. Methods A total of 3512 patients underwent head and neck cancers radical resection from 2013 to 2019. A one-to-three control group without postoperative PE was selected matched by age, gender, and type of cancer. Univariate analyses were performed for the perioperative patient data including hemodynamic management factors. Conditional logistic regression was used to analyze the factors and their odds ratios. Results Postoperative PE was prevalent in 0.85% (95%CI = 0.56-1.14). Univariate analyses showed that a high ASA grade, high BMI, and smoking history may be related to postoperative PE. There was significantly difference in operation time between the two groups, especially for> 4 h [22(78.6%) vs 43(51.2%), P = .011]. The urine output was lower [1.37(0.73-2.21) ml center dot kg(- 1)center dot h(- 1) vs 2.14(1.32-3.46) ml center dot kg(- 1)center dot h(- 1), P = .006] and the incidence of oliguria was significantly increased (14.3% vs 1.2%, P = .004) in the PE group. Multivariable conditional logistic regression showed postoperative PE were associated with the cumulative duration for intraoperative hypotension (OR = 2.330, 95%CI = 1.428-3.801, P = .001), oliguria (OR = 14.844, 95%CI = 1.089-202.249, P = .043), and operation time > 4 h (OR = 4.801, 95%CI = 1.054-21.866, P = .043). Conclusions The intraoperative hypotension, oliguria, and operation time > 4 h are risk factors associated with postoperative PE after radical resection of head and neck cancers. Improving intraoperative hemodynamics management to ensure adequate blood pressure and urine output may reduce the occurrence of such complications.