In this study, the electric field and the particle precipitation at different spatial scale sizes have been investigated by utilizing the Dynamic Explorer 2 satellite data set, focusing on conditions of moderately strong southward interplanetary magnetic field. Dynamic Explorer 2 data from the period between 1981 and 1983, from all universal times, seasons, and both hemispheres, have been processed and binned over geomagnetic latitude and local time. It is found that, as compared with the large‐scale (>500 km) average electric field and particle precipitation, the variabilities (i.e., departures from the large‐scale average) of electric field and particle precipitation are not negligible. Moreover, the electric field variability tends to be anticorrelated with the particle precipitation variability in the auroral regions on small scale and mesoscale (<500 km). The impacts associated with the small‐scale and mesoscale electric field and particle precipitation variabilities on Joule heating have also been addressed in this study by using the Global Ionosphere and Thermosphere Model. It is found that although Joule heating can be significantly enhanced by the small‐scale and mesoscale electric field variabilities (~27% globally), the corresponding change in the particle precipitation tends to depress such enhancement (−5% globally), which is not negligible on the dusk side (up to −17.5% locally). It is the first time that the correlation between electric field and particle precipitation variabilities on small scale and mesoscale has been quantified. Furthermore, the impact on Joule heating associated with the correlation between the small‐scale and mesoscale electric field and particle precipitation variabilities has been evaluated unprecedentedly in a general circulation model. Plain Language Summary At high latitudes, the electromagnetic energy from the magnetosphere dissipates into Earth's upper atmosphere, leading to both local and global changes. The accuracy of numerical simulation of Earth's upper atmosphere depends on the accuracy of the estimation of such energy input or heating, which is always challenging. The heating is closely related with the ionospheric electric field and precipitating particles from the magnetosphere. Part of the difficulty of determining the heating is that the knowledge about their structures below the model resolution (i.e., small‐scale and mesoscale variabilities) is still limited, especially about their correlation. Therefore, it is still unclear to what extent such correlation can impact the heating estimation. In this study, the correlation between small‐scale and mesoscale electric field and particle precipitation variabilities has been quantified for the first time by utilizing satellite observations. Furthermore, the impact of small‐scale and mesoscale variabilities and their correlation on the heating estimation has been evaluated unprecedentedly using a general circulation model. It is found that there can be a large localized overestimation of heating if the correlation between small‐scale and mesoscale electric field and particle precipitation variabilities is neglected. Our results can be useful for the improvement of numerical models of Earth's upper atmosphere and important for magnetosphere‐ionosphere coupling studies. Key Points The electric field and particle precipitation variabilities at high latitudes have been quantified The variable electric field is anticorrelated with the variable particle precipitation on small scale and mesoscale The reduction of Joule heating due to the anticorrelation between the small‐scale and mesoscale electric field and particle precipitation variabilities is not negligible