Objective To comparatively analyze the rationality of emergency medication after Wenchuan earthquake with that after Lushan earthquake in West China Hospital of Sichuan University, based on the use of medicine of the victim’s disease spectrum. Method By using Excel, defined daily dose system (DDDs) and drug utilization index (DUI) were used as the evaluation indexes to analyze the rationality of emergency medication in West China Hospital of Sichuan University within one month after Wenchuan earthquake and Lushan earthquake. Results Within one month after Wenchuan and Lushan earthquake, there were 1 839 and 488 victims treated in the hospital, respectively. Within one month after the two earthquakes, the variation tendency of DDDs of drugs and number of victims was consistent, and the consistency was better in Lushan earthquake than that in Wenchuan earthquake. Among the 60 drugs which DDDs were ranked top five in their pharmacological class (top ten for antimicrobials) in Wenchuan earthquake, the majority of them were injections (injections vs. non-injections: 70.0% vs. 30.0%); the results showed that the medication (DUI=1) only accounted for 10.0%, the medication (DUI<1) accounted for 28.3%, which implied that the use of drugs was insufficient, the medication (DUI>1) accounted for 61.7%, which implied that drugs were overused; the average of DUI was 1.61. And in Lushan earthquake, injections also accounted for a larger proportion than non-injections (63.3%vs. 36.7%); the results showed that the medication (DUI=1) accounted for 15.0%, the medication (DUI<1) accounted for 38.3%, the medication (DUI>1) accounted for 46.7%; the average of DUI was 1.30. Conclusions Base on the DUI, we draw the conclusion that the rationality of emergency drug use and the timeliness of emergency drug supply were better in Lushan earthquake than those in Wenchuan earthquake. But the rationality of using the DUI, which is an evaluation index for normal conditions, to evaluate the emergency conditions still needs to be further verified.