Nymphaea hybrid, a precious water lily, is a widely-cultivated aquatic flower with high ornamental, economic, medicinal, and ecological value; it blooms recurrently and emits a strong fragrance. In the present study, in order to understand the volatile components of N. hybrid and its relationship with petals structure characteristics, the morphologies and anatomical structures of the flower petals of N. hybrid were investigated, and volatile compounds emitted from the petals were identified. Scanning and transmission electron microscopy were used to describe petal structures, and the volatile constituents were collected using headspace solid-phase microextraction (HS-SPME) fibers and analyzed using gas chromatography coupled with mass spectrometry (GC-MS). The results indicated that the density and degree of protrusion and the number of plastids and osmiophilic matrix granules in the petals play key roles in emitting the fragrance. There were distinct differences in the components and relative contents of volatile compounds among the different strains of N. hybrid. In total, 29, 34, 39, and 43 volatile compounds were detected in the cut flower petals of the blue-purple type (Nh-1), pink type (Nh-2), yellow type (Nh-3) and white type (Nh-4) of N. hybrid at the flowering stage, with total relative contents of 96.78%, 97.64%, 98.56%, and 96.15%, respectively. Analyses of these volatile components indicated that alkenes, alcohols, and alkanes were the three major types of volatile components in the flower petals of N. hybrid. The predominant volatile compounds were benzyl alcohol, pentadecane, trans-α-bergamotene, (E)-β-farnesene, and (6E,9E)-6,9-heptadecadiene, and some of these volatile compounds were terpenes, which varied among the different strains. Moreover, on the basis of hierarchical cluster analysis (HCA) and principal component analysis (PCA), the N. hybrid samples were divided into four groups: alcohols were the most important volatile compounds for Nh-4 samples; esters and aldehydes were the predominant volatiles in Nh-3 samples; and ketones and alkenes were important for Nh-2 samples. These compounds contribute to the unique flavors and aromas of the four strains of N. hybrid.