Recent Atacama Large Millimeter and Submillimeter Array (ALMA) observations of the protoplanetary disk around the Herbig Ae star HD 163296 revealed three depleted dust gaps at 60, 100, and 160 au in the 1.3 mm continuum as well as CO depletion in the middle and outer dust gaps. However, no CO depletion was found in the inner dust gap. To examine the planet–disk interaction model, we present results of 2D two fluid (gas + dust) hydrodynamic simulations coupled with 3D radiative transfer simulations. To fit the high gas-to-dust ratio of the first gap, we find that the Shakura–Sunyaev viscosity parameter α must be very small (≲10−4) in the inner disk. On the other hand, a relatively large α (∼7.5×10−3) is required to reproduce the dust surface density in the outer disk. We interpret the variation of α as an indicator of the transition from an inner dead zone to the outer magnetorotational instability (MRI) active zone. Within ~100 au, the HD 163296 disk's ionization level is low, and non-ideal magnetohydrodynamic effects could suppress the MRI, so the disk can be largely laminar. The disk's ionization level gradually increases toward larger radii, and the outermost disk (r>300 au) becomes turbulent due to MRI. Under this condition, we find that the observed dust continuum and CO gas line emissions can be reasonably fit by three half-Jovian-mass planets (0.46, 0.46, and 0.58MJ) at 59, 105, and 160 au, respectively.