Monoterpenoids with “cage-like” pinane skeleton are the unique and main bioactive constituents in peony root, the root of Paeonia lactiflora. A liquid chromatography coupled with ion trap and time-of-flight mass spectrometry (LC-IT-TOF-MS) method was developed for characterization and quantification of monoterpenoids in different types of peony root and the roots of related Paeonia species. MS/MS fragmentation patterns of monoterpenoids with paeoniflorin-, albiflorin- and sulfonated paeoniflorin-type of skeletons were elucidated, which provided basic clues enabling subsequent identification of 35 monoterpenoids in LC-MS profiles of Paeonia species. The profiling analysis and further quantification of 15 main monoterpenoids in 56 samples belonged to red peony root (RPR), white peony root (WPR), peony root in Japanese market (PR) and the roots of related Paeonia species revealed that paeoniflorin, benzoylpaeoniflorin, galloylpaeoniflorin, oxypaoniflorin and albiflorin were predominant constituents in all the samples; mudanpioside C was the characteristic component of P. lactiflora, and 4-O-methyl-paeoniflorin was only detected in P. veitchii and P. anomala. Total contents of the 15 monoterpenoids were obviously higher in the roots of P. lactiflora and P. veitchii than in those of P. anomala and P. japonica. Principal component analysis based on the quantitative results showed that the samples derived from P. lactiflora were clearly classified into RPR, WPR/PR, and sulfur-fumigated WPR groups, besides the respective group of P. veitchii and P. anomala. This study clarified the chemical characteristics of the respective type of peony root and the related Paeonia species, as well as the marker constituents for their discrimination.