Abstract. Biogenic volatile organic compounds (BVOCs) simulated by current air quality and climate models still have large uncertainties, which can influence atmosphere chemistry and secondary pollutant formation over East China. These uncertainties are generally resulted from two sources. One is from different biogenic emission schemes coupled in model, representing for different treatments of physical and chemistry progresses during the emissions of BVOCs. The other is from the biased distribution of vegetation types over a specific region. In this study, the version of WRF-Chem updated by the University of Science and Technology of China (USTC version of WRF-Chem) from the public WRF-Chem(v3.6) is used. The modeling results over East China with different versions (v1.0, v2.0, v3.0) of Model of Emissions of Gases and Aerosols from Nature (MEGAN) in WRF-Chem are examined and documented. Sensitivity experiments with these three versions of MEGAN and two vegetation datasets are conducted to investigate the difference of three MEGAN versions in modeling biogenic VOCs and its dependence on the vegetation distributions. The experiments are also conducted for spring (April) and summer (July) to examine the seasonality of the modeling results. The results indicate that MEGANv3.0 simulates the largest amount of biogenic isoprene emissions over East China. The different performance among MEGAN versions is primarily due to their different treatments of applying emission factors and vegetation types. In particular, the results highlight the importance of considering sub-grid vegetation fraction in estimating BVOCs emissions. Among all activity factors, temperature-dependent factor dominates the seasonal change of activity factor in all three versions of MEGAN, while the different response to the leaf area index (LAI) change determines the difference among the three versions in seasonal variation of BVOC emissions. The simulated surface ozone concentration due to BVOCs can be significantly different among the experiments with three versions of MEGAN, which is mainly due to their impacts on surface VOCs and NOx concentrations. This study suggests that there is still large uncertain range in modeling BVOCs and their impacts on photochemistry and ozone production. More accurate vegetation distribution and measurements of biogenic emission flux and species concentration are needed to evaluate the model performance and reduce the uncertainties.