The conventional Ensemble Kalman filter (EnKF), which is now widely used to calibrate emission inventories and to improve air quality simulations, is susceptible to simulation errors of meteorological inputs, making accurate updates of high temporal-resolution emission inventories challenging. In this study, we developed a novel meteorologically adjusted inversion method (MAEInv) based on the EnKF to improve daily emission estimations. The new method combines sensitivity analysis and bias correction to alleviate the inversion biases caused by errors of meteorological inputs. For demonstration, we used the MAEInv to inverse daily carbon monoxide (CO) emissions in the Pearl River Delta (PRD) region, China. In the case study, 60% of the total CO simulation biases were associated with sensitive meteorological inputs, which would lead to the overestimation of daily variations of posterior emissions. Using the new inversion method, daily variations of emissions shrank dramatically, with the percentage change decreased by 30%. Also, the total amount of posterior CO emissions estimated by the MAEInv decreased by 14%, indicating that posterior CO emissions might be overestimated using the conventional EnKF. Model evaluations using independent observations revealed that daily CO emissions estimated by MAEInv better reproduce the magnitude and temporal patterns of ambient CO concentration, with a higher correlation coefficient (R, +37.0%) and lower normalized mean bias (NMB, -17.9%). Since errors of meteorological inputs are major sources of simulation biases for both low-reactive and reactive pollutants, the MAEInv is also applicable to improve the daily emission inversions of reactive pollutants.