Digital holographic microscopy (DHM) provides a non-destructive measurement technique based on calculation of optical path length changes of the sample under study. If the changes are caused by refractive index variations within a constant physical thickness, the technique results in the precise measurement of the refractive index . In this paper, DHM is utilized to map the refractive index over a wide surface of a T-shaped micro channel. The micro channel is filled up by a solution of two chemical reactant fluids. In some chemical reactions the refractive index of the resultant may be highly different from the refractive indices of the reactants. Using microinjection pumps methane and water as reactants are injected into the channel at the same flow rates. Changes in optical path ways are measured by live recording the digital holograms during the fluids interaction for all the field of view pixels. The holograms are recorded by a detector and post processed by a computer in order to reconstruct the phase profile changes though angular spectrum propagation method. The changes in the refractive indices that take place during the reaction process, are viewed by the detector and are calculated and mapped for the T channel and Y channel.