Background Effect of atmospheric CH₄ mole fraction on sea-to-air CH₄ flux was important for assessment of carbon emissions, while it was paid little attention and lack of quantification. Results According to the method described by Wanninkhof (2014), the impacts of three different atmospheric CH₄ data on the calculated sea-to-air CH₄ flux were evaluated. Results showed that, compared to data observed at the Tae-ahn Peninsula station and the simulated MBL-CH₄ references, in situ observed atmospheric CH₄ mole fraction was 132 and 140 nmol/mol higher in July 2013, and 98 and 132 nmol/mol higher in February 2017 in the Bohai Sea, respectively. The different applied atmospheric CH₄ mole fraction induced mean deviations of 1.5 µmol/m²/day in July 2013 and 1.0 µmol/m²/day in February 2017, respectively. In addition, effects of difference among three atmospheric CH₄ mole fractions could result in greater deviations of calculated sea-to-air CH₄ flux in summer in coastal shallow waters than that in winter in deep regions or open oceans. Conclusions From the perspective of narrowing the uncertainty of carbon emission, it was essential to calculate sea-to-air CH₄ flux by using the field observed atmospheric CH₄ mole fraction, especially in coastal shallow seas.