Objective To analyze detailed records of peasants’ hospitalization and compensation due to external causes of illness and death based on a county’s new rural cooperative medical scheme (NRCMS) from 2009 to 2010. Methods We systematically acquired the relevant record data of all inpatients via the management information system of NRCMS in this county. According to ICD-10 coding, we categorized and divided diseases into groups in basis of discharge diagnosis of each inpatient. Data were analyzed using SPSS 17.0. Results Inpatients due to external causes of illness and death who participated in the NRCMS accounted for 17.4% (7 913/45 432) of the total inpatient person-time in 2009 and 20.7% (12 568/60 643) in 2010. External causes of illness and death ranked the first in the hospitalization disease spectrum, which mainly were animal bites and accidental injuries. About 20% of their hospitalization expense was compensated by the NRCMS. More than half of the inpatients could be hospitalized for the treatment in the county township health center (59.6% in 2009 and 66.8% in 2010). Conclusion The result of this study indicates that external causes of illness and death including animal bites and accidental injuries have been a major health problem that peasants in this county face.