Measurements collected from ground monitoring stations have gained popularity as a valuable data source for evaluating numerical models and correcting model errors through data assimilation. The penalty quantified by simulation minus observations drives both model evaluation and assimilation. However, the penal forces are challenged by the existence of a spatial-scale disparity between model simulations and observations. Chemical transport models (CTMs) divide the atmosphere into grid cells, providing a structured way to simulate atmospheric processes. However, their spatial resolution often does not match the limited coverage of in situ measurements, especially for short-lived air pollutants. Within a broad grid cell, air pollutant concentrations can exhibit significant heterogeneity due to their rapid generation and dissipation. Ground observations with traditional methods (including “nearest search” and “grid mean”) are less representative when compared to model simulations. This study develops a new land-use-based representative (LUBR) observational operator to generate spatially representative gridded observations for model evaluation. It incorporates high-resolution urban–rural land use data to address intra-grid variability. The LUBR operator has been validated to consistently provide insights that align with satellite Ozone Monitoring Instrument (OMI) measurements. It is an effective solution to accurately quantify these spatial-scale mismatches and further resolve them via assimilation. Model evaluations with 2015–2017 NO2 measurements in the study area demonstrate that biases and errors differed substantially when the LUBR and other operators were used, respectively. The results highlight the importance of considering fine-scale urban–rural differences when comparing models and observations, especially for short-lived pollutants like NO2.