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An iterative dynamic initialization method is presented to produce balanced initial conditions for whole atmospheric global modeling. In this method, a global hydrostatic numerical model is iteratively nudged toward ground‐to‐space wind and temperature profiles at specific date and time. Ground‐to‐space atmospheric profiles are obtained by fitting spline curves to reanalyses below the lower mesosphere and empirical model results in the upper atmosphere. An optimal nudging coefficient is determined by examining if reasonable structure of mesospheric gravity wave (GW) momentum forcing and residual mean meridional circulations can be obtained from balanced initial conditions. Estimated mesospheric GW momentum forcing is found to exhibit a distinctive structure with larger (smaller) values in the lower and upper mesosphere (in the midmesosphere), when compared with parameterized climatological forcing. The iterative dynamic initialization allows for dynamical balance among the model's prognostic variables and reduces excitation of spurious GWs and noises at initial time. However, theoretical imbalances, measured by the ellipticity of the nonlinear balance equation, are not completely eliminated in balanced flows, and they are found in narrow tropospheric frontal regions and over localized areas associated with the large‐scale instability in the midlatitude middle atmosphere. These imbalances are discussed in the context of their potential relation to generation of planetary‐scale and inertia GWs around the middle atmospheric and tropospheric jets. Plain Language Summary: This study reports a method of initializing a whole‐atmosphere global model that covers from the ground to the lower thermosphere. Through this initialization, a whole atmospheric state balanced with the model dynamics is effectively generated. Free coefficient required for the initialization is chosen by estimating gravity wave momentum forcing and meridional mass circulations in the mesosphere and lower thermosphere. In the generated balanced flow, theoretical imbalances, measured by the ellipticity of the nonlinear balance equation, are found. These imbalances can be related to the spontaneous generation of gravity waves and balanced and unbalanced large‐scale instabilities in the middle atmosphere. The large‐scale instabilities can be attributed to generation of the planetary‐scale and inertia gravity waves in the middle atmosphere. Key Points: Iterative dynamic initialization for whole atmospheric global modeling is presentedGravity wave momentum forcing and mass circulations are estimated to constrain nudging coefficientDeviations from nonlinear balance may occur in association with large‐scale instabilities [ABSTRACT FROM AUTHOR]