Humic acid originating from lignite is a popular resource of organic fertilizer. The effects of humic acid application on crop biomass and soil CO 2 emission charged the regional agro-ecosystem carbon balance. Two kinds of humic acid, obtained from lignite via H 2 O 2 -oxidation (OHA) and KOH-activation (AHA), were applied in a wheat-maize rotation located field at three levels of 500 (OHA1; AHA1), 1000 (OHA2; AHA2), and 1500 kg hm−2 (OHA3; AHA3), only chemical fertilizer treatment (CF) as control to investigate the change of soil CO 2 emission, crop yield and ecosystem carbon balance in 2016–2019. During the four experimental years, the trend of cumulative efflux of soil CO 2 was increasing in medium and high dosage humic acid treatments. The grain yield of wheat and maize had the same trend as the cumulative efflux of soil CO 2 due to the increase of soil NO 3 −-N and soil available P directly affected by humic acid application. The main factor of cumulative soil CO 2 efflux improvement was soil NO 3 −-N and soil available P in 2016, while soil available potassium became key factor in 2019 with the step regression. Net ecosystem productivity (NEP) was used to assess ecosystem carbon balance, which was positive values showed atmospheric CO 2 sink under all the fertilization treatments and increased with the increase of humic acid use level. AHA2 and AHA3 treatments charged the higher NEP in 2019 than 2016. Meanwhile, AHA treatment presented a higher NEP average than OHA treatment with the same applied level. Crop yield and soil available P was the directly positive factor to NEP over four years under the fertilization by SEM analysis. It is recommended that AHA be applied at 1000 kg hm−2 together with chemical fertilizers to achieve the higher crop yield and a sink of the atmospheric CO 2 in agricultural fields in North China. [Display omitted] • Humic acid treatment promoted the rate and cumulative quantity of soil CO 2 emission. • Soil available nutrients induced soil CO 2 emission with humic acid fertilization. • Crop yield and soil available P directly had positive effect on NEP by SEM analysis. • Humic acid activated by KOH charged higher NEP than with H 2 O 2 -oxidation. [ABSTRACT FROM AUTHOR]