Oil-tea belongs to the Camellia genus, an important oil crop in China. However, oil-tea is taxonomically challenging due to its morphological variation, polyploidy, and interspecific hybridization. Therefore, the present study aimed to investigate the flower organs’ morphology and pollen micro-morphology of 18 oil-tea genotypes in detail and discussed their significance for oil-tea taxonomy. The quantitative parameters of flowers were measured using Vernier caliper measurements. Pollen morphology was observed and photographed using scanning electron microscopy (SEM). The results indicated that the flower size varied significantly among the tested oil-tea genotypes, with the corolla diameter ranging from 42.25 μm in C. meiocarpa ‘LP’ to 89.51 μm in C. oleifera ‘ASX09’. The pollen grains of oil-tea are monads and medium grade in pollen size. There were two types of polar views, including triangular or subcircular, with a polar axis length (P) ranging from 27.5 μm in C. oleifera ‘CY67’ to 59.04 μm in C. mairei (H. Lév.) Melch. var. lapidea (Y.C. Wu) Sealy. The equatorial views exhibited oblate, spherical, or oblong shapes, with an equatorial axis length (E) of 21.32 to 41.62 μm. The pollen exine sculpture was perforate, verrucate, and reticulate. The perforation lumina diameter (D) ranged from 0.29 μm in C. magniflora Chang to 1.22 μm in C. yuhsienensis Hu, and the perforation width (W) varied from 0.77 μm in C. osmantha to 1.40 μm in C. gauchowensis ‘HM349’, respectively. Qualitative clustering analysis (Q-type cluster) and principal component analysis (PCA) were conducted using eleven indexes of flower and pollen morphology, and the 18 oil-tea genotypes were classified into three categories. In addition, the correlation analysis showed that there was a significant correlation between pollen size and flower morphology or pollen exine sculpture. These results offer valuable information on the classification and identification of the 18 oil-tea germplasm resources.