Context. The inner few au region of planet-forming disks is a complex environment. High angular resolution observations have a key role in understanding the disk structure and the dynamical processes at work. Aims. In this study we aim to characterize the mid-infrared brightness distribution of the inner disk of the young intermediate-mass star HD 163296, from VLTI/MATISSE observations. Methods. We use geometric models to fit the data. Our models include a smoothed ring, a flat disk with inner cavity, and a 2D Gaussian. The models can account for disk inclination and for azimuthal asymmetries as well. We also perform numerical hydro-dynamical simulations of the inner edge of the disk. Results. Our modeling reveals a significant brightness asymmetry in the L-band disk emission. The brightness maximum of the asymmetry is located at the NW part of the disk image, nearly at the position angle of the semimajor axis. The surface brightness ratio in the azimuthal variation is $3.5 pm 0.2$. Comparing our result on the location of the asymmetry with other interferometric measurements, we confirm that the morphology of the $r<0.3$ au disk region is time-variable. We propose that this asymmetric structure, located in or near the inner rim of the dusty disk, orbits the star. For the physical origin of the asymmetry, we tested a hypothesis where a vortex is created by Rossby wave instability, and we find that a unique large scale vortex may be compatible with our data. The half-light radius of the L-band emitting region is $0.33pm 0.01$ au, the inclination is ${52^circ}^{+5^circ}_{-7^circ}$, and the position angle is $143^circ pm 3^circ$. Our models predict that a non-negligible fraction of the L-band disk emission originates inside the dust sublimation radius for $mu$m-sized grains. Refractory grains or large ($gtrsim 10 mu$m-sized) grains could be the origin for this emission.
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