We used ultra-performance liquid chromatography-mass spectrometry (I-Class UPLC/Xevo TQ MS) to separate and identify the flavonoids in lotus pollens from 50 cultivars. Lotus pollen contains 13 flavonols and 2 flavones, all reported in lotus pollen for the first time. The most abundant flavonoids were quercetin glucosides, namely quercetin 3-O-glucuronide, quercetin 3-O-rhamnopyranosyl-(1→2)-glucopyranoside and quercetin 3-O-arabinopyranosyl-(1→2)- galactopyranoside, detected in all cultivar pollen. The total flavonoid (TF) content ranged from 82.64 to 281.08 mg∙100 g^-1 in 50 cultivars, with Fei-Yun-Qian-Ye showing the highest TF and Xian-Nv-San-Hua the lowest. According to cluster analysis, 50 lotus cultivars were classified into four groups; group B contained more flavonoids than other groups, and group B TF content was the highest. TF content in Fei-Yun-Qian-Ye, Bo-Li-Xiao-Jie and Shu-Hong-Lian exceeded 200 mg∙100 g^-1 dry weight and could be developed into lotus pollen products.