Objective This study aimed to investigate the clinical characteristics and long-term prognosis of mycoplasma pneumoniae pneumonia (MPP)-associated thrombosis and to gain a better understanding of the diagnosis and treatment of the disease. Methods The medical records of 14 children with MPP-associated thrombosis between January 2016 and April 2020 were retrospectively reviewed at the Tianjin Children’s Hospital. Results The ages of the patients ranged from 3 to 12 years old. Among the 14 cases, there were five cases of pulmonary embolism, two cases of cerebral infarction, one case of splenic infarction, one case of cardiac embolism, two cases of cardiac embolism with comorbid pulmonary embolism, one case of internal carotid artery and pulmonary embolism, one case of combined internal carotid artery and the cerebral infarction, and one case combined cardiac embolism and lower limb artery embolism. All cases had elevated D-dimer levels. After thrombolysis and anticoagulation therapy, three cases with cerebral embolism still suffered from neurological sequelae. In contrast, the remaining cases did not develop complications. Conclusion MPP-associated thrombosis can occur in any vessel of the body. Thrombosis-associated symptoms may be complex and non-specific. Elevated D-dimer levels in a child with refractory mycoplasma pneumoniae pneumonia should raise suspicion of thrombosis. The long-term prognosis of thrombosis was favorable after the timely administration of anticoagulant therapy.