Toosendan Fructus with various pharmaceutical activities is a good source for the finding of new bioactive components, especially limonoids inside have been reported to have anticancer and antifeedant activities. To find more potential new bioactive compounds, the mass spectrometric characteristics of nimbolinin-type limonoids were first investigated. Utilizing these characteristics, totally 60 nimbolinins, including 33 new ones and at least 10 bioactive compounds, were identified by ultra-high performance liquid chromatography-quadrupole-time-of-flight mass spectrometry (UHPLC-Q-TOF/MS). Furthermore, based on UHPLC-Q-TOF/MS and statistical analysis, 9 limonoids were identified to be the differential components between Toosendan Fructus and Azedarach Fructus. Particularly, nimbolinin A and toosendanin (TSN) with higher content in Azedarach Fructus and Toosendan Fructus respectively should be good markers. Finally, an UHPLC-triple quadrupole mass spectrometry (UHPLC-QQQ/MS) quantification approach for nimbolinin A and TSN was developed for their quality control. These results provided the basis for drug development and quality control of Toosendan Fructus and Azedarach Fructus.