The seed kernels and hulls of Paeonia lactiflora Pall. (Chinese peony) contain numerous bioactive compounds. We extracted monoterpene glycosides and oligostilbenes from three varieties of P. lactiflora seed kernels and hulls, and analysed the bioactive compounds in these samples. The results indicated that seed kernels contained significant concentrations of monoterpene glycosides, whilst seed hulls contained high concentrations of oligostilbene compounds. The profiles of monoterpene glycosides and oligostilbene compounds in extracts were significantly dependent on the P. lactiflora variety. Ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry and reference to literature data enabled 96 compounds to be tentatively characterised, including 24 monoterpene glycosides, 16 oligostilbene compounds, and several phenolic compounds, iridoid glycosides, diterpenoids and triterpenoids. This is the first study to find most of these compounds in P. lactiflora seed kernels and hulls. Paeoniflorin (1779.61 ± 10.33 mg/100 g) was the predominant monoterpene glycoside in seed kernels, whilst hulls had the highest concentrations of sufruticosol A (791.93 ± 25.09 mg/100 g) and trans-ε-viniferin (607.4 ± 16.22 mg/100 g). All of the results confirmed that P. lactiflora seed kernels and hulls contain substantial concentrations of natural products. These products may be useful as medicines or as ingredients in functional foods.