Longxuetongluo Capsule (LTC), which is derived from the total phenolic extract of Chinese dragon’s blood, has been proved to be safe as well as effective towards ischemic stroke. However, the effective material basis remains unclear. The present study thereby focused on the clarification of the qualitative and quantitative properties for the phenolic derivatives in LTC. Regarding homolog-focused chemical profiling, the mass fragmentation patterns of the primary subtypes of phenolic compounds such as homoisoflavanones, flavanes, chalcones, and flavonoid oligomers were summarized by assaying authentic references with hybrid ion trap time-of-flight mass spectrometry, and the chemical structures of 124 phenolic compounds, in total, were unambiguously or tentatively annotated in LTC by matching the accurate mass spectral profiles with the proposed mass cracking rules and those reference substances. Afterwards, simultaneous determination of 12 primary phenolic compounds was carried out in different batches of LTC using HPLC-DAD, after that the method was proved to be accurate, precise, and reproducible according to diverse method validation assays. The obtained findings are expected to be meaningful for clarifying the effective substances and quality assessment of LTC.