Abstract Recent observations have detected excess Hα emission from young stellar systems with an age of several Myr such as PDS 70. One-dimensional radiation-hydrodynamic models of shock-heated flows that we developed previously demonstrate that planetary accretion flows of >a few ten km s⁻¹ can produce Hα emission. It is, however, a challenge to understand the accretion process of proto-giant planets from observations of such shock-originated emission because of a huge gap in scale between the circumplanetary disk (CPD) and the microscopic accretion shock. To overcome the scale gap problem, we combine two-dimensional, high-spatial-resolution global hydrodynamic simulations and the one-dimensional local radiation-hydrodynamic model of the shock-heated flow. From such combined simulations for the protoplanet–CPD system, we find that the Hα emission is mainly produced in localized areas on the protoplanetary surface. The accretion shocks above the CPD produce much weaker Hα emission (approximately one to two orders of magnitude smaller in luminosity). Nevertheless, the accretion shocks above the CPD significantly affect the accretion process onto the protoplanet. The accretion occurs at a quasi-steady rate if averaged on a 10 day timescale, but its rate shows variability on shorter timescales. The disk surface accretion layers including the CPD shocks largely fluctuate, which results in the time-variable accretion rate and Hα luminosity of the protoplanet. We also model the spectral emission profile of the Hα line and find that the line profile is less time-variable despite the large variability in luminosity. High-spectral-resolution spectroscopic observation and monitoring will be key to revealing the property of the accretion process.