The after-harvesting sun-dried processing of Fritillariae thunbergii bulbus (Zhebeimu) was the traditional treatment for commodity. Over recent decades the natural drying process for bulbus of Fritillariae has been replaced by sulfur-fumigation for reducing the drying duration and pest control. We used ultra-performance liquid chromatography coupled with evaporative light scattering detection (UPLC-ELSD) fingerprinting analysis and major alkaloids determination to investigate the potential damaging effect of the sulfur-fumigating process. The experimental conditions were as follows: Chromatography was proceeded on Waters Acquity UPLC BEH C(18) column; the linear gradient elution was conducted with mobile phase prepared from acetonitrile-0.02% triethylamine; the drift tube temperature was set at 40°C with a nitrogen flow-rate of 30psi, and the spray parameter was set 40%. All calibration curves showed good linear regression (R>0.9991) within the tested range. The method was validated for precision, accuracy, limit of detection and quantification. The study also has shown that sulfur-fumigated samples had significant loss of the main active compounds and a more destructive fingerprint profile when compared to the sun-dried samples.