Objective:To understand the drug treatment status of echinococcosis patients in Jimusar County, Changji Prefecture, Xinjiang, and to explore the construction of medical cooperation system for echinococcosis patients, and to provide reference for optimization and popularization of medical cooperation system.Methods:Data of echinococcosis patients registered in Jimusar Center for Disease Control and Prevention from 2009 to 2018 were collected. The data of patients' medical records and follow-up information were collected by the principle of double entry. The research methods of combining quantitative and qualitative methods were applied to investigate the baseline of patient prevention and treatment system (including regional distribution, education level, recurrence, follow-up medication, etc). Follow-up was conducted on the whole treatment process of echinococcosis patients in the pilot counties, and comparative analysis was made on the treatment situation before and after the use of medical cooperation system. Logistic regression model was used to analyze the indicators that might affect the follow-up effect. Semistructured questionnaire survey was used to analyze the implementation effect of the medical cooperation system.Results:Patients were mainly distributed in rural areas (81.48%, 154/189), mostly in high schools and below (94.18%, 178/189), 39.68% (75/189) were relapsed and treated again, and 68.25% (129/189) were treated with non-standard medication. Influencing factors of effective follow-up medication in echinococcosis patients showed that patients with no side effects, abnormal liver function during follow-up, two or more times of B-ultrasound examination and multiple cysts had higher effective follow-up medication rate ( P < 0.01 or < 0.05). After the implementation of the integrated medical cooperation system, the proportion of unknown stages of diagnosis of cystic echinococcosis in Jimusar County decreased by 60.18%. The pilot counties initially formed a management model of echinococcosis patients based on outpatient, disease control and health centers. Conclusions:Echinococcosis patients have high recurrence rate in Jimusar County, and the effective follow-up medication rate is low. The medical cooperation system for echinococcosis patients in Xinjiang is explored, and the working mechanism of medical institutions linked with disease control institutions is formed. The working model suggestion is put forward, which could provide a scientific basis for further promotion and comprehensive evaluation of the medical cooperation system.