Collagen is one of the most common materials used to form scaffolds for tissue engineering applications. The multi-channel collagen gel (MCCG) obtained by the dialysis of an acidic collagen solution in a neutral buffer solution has a unique structure, with many capillaries of diameters several tens to a few hundred micrometers, and could be a potential candidate as a biomimetic scaffold for three-dimensional tissue engineering. In the present study, the formation of MCCG was investigated by in situ rheological measurements based on a particle tracking method (particle tracking microrheology, PTM). PTM enabled us to measure changes in the rheological properties of collagen solutions under the continuous exchange of substances during dialysis. When an observation plane was set perpendicular to the direction of gel growth, we first observed convectional flow of the collagen solution, followed by phase separation and gelation. We showed that the structure of the MCCG originated from the transient structure formed during the initial stage of viscoelastic phase separation and was fixed by the subsequent gelation.