Satellite-driven inversions provide valuable information about methane (CH4) fluxes, but the assimilation of total column-averaged dry-air mole fractions of CH4 (XCH4) has been challenging. This study explores, for the first time, the potential of the new lower-tropospheric partial column (pXCH4_LT) GOSAT data, retrieved by the Japan Aerospace Exploration Agency (JAXA), to constrain global and regional CH4 fluxes. Using the CarbonTracker Europe-CH4 (CTE-CH4) atmospheric inverse model, we estimated CH4 fluxes between 2016–2019 by assimilating the JAXA/GOSAT pXCH4_LT and XCH4 data and surface CH4 observations independently of each other. The Northern Hemisphere CH4 fluxes derived from the pXCH4_LT data were similar to the estimates derived from the surface observations but were underestimated by about 35 Tg CH4 yr−1 (∼ 6 % of the global total) using the XCH4 data. For the Southern Hemisphere, the estimates from both GOSAT inversions were about 15–30 Tg CH4 yr−1 higher than those derived from surface data. The evaluations against independent data from the Atmospheric Tomography Mission aircraft campaign showed good agreement in the lower-tropospheric CH4 from the inversions using the pXCH4_LT and surface data. However, from these inversions, the modelled north–south gradients showed significant overestimation in the upper troposphere and stratosphere, possibly due to relatively uniform inter-hemispheric OH distributions that control CH4 sinks. Overall, we found that the use of the JAXA/GOSAT pXCH4_LT data shows considerable potential in constraining global and regional CH4 fluxes, advancing our understanding of the CH4 budget.