Given the key role of bees as indicators for environmental assessment, residues in bees and bee products have attracted great interest. In this regard, an improved, highly sensitive method for quantifying the insecticide pyriproxyfen and its four metabolites (4′-OH-Pyr, DPH-Pyr, 2-OH-PY, 4′-OH-POP) in honeybees, larvae, and bee products (honey, pollen, royal jelly and wax) should be established. For this purpose, we used ultra-performance liquid chromatography coupled with triple-quadrupole mass spectrometry for rapid quantification (≤5 min). Recoveries for various matrices ranged from 73.77% to 114.97%, with satisfactory intra-day and inter-day precision (relative standard deviations of 0.03–8.61% and 0.10–7.25%, respectively). The results demonstrated excellent linearity (R² > 0.9903) with a limit of quantification of 1 μg/kg for six different matrices. We collected and analyzed 597 samples (honey, bees and wax) from four major beekeeping areas in China. Only 47 of these samples contained residues of pyriproxyfen and two of its metabolites (2-OH-PY, 4′-OH-Pyr), and high levels of contamination were found in bee samples (2–739 μg/kg), with substantive accumulation in wax (levels were 9.49% higher than in other samples). The result demonstrate that the method provides a reliable and convenient means of monitoring pyriproxyfen and its metabolites in bee products for better product quality, human health, and international commercial competition and also lays a foundation for risk assessment of potential pyriproxyfen contamination in China.