Mixing behavior is critical for enhancing the selectivity of fast chemical reactions in microreactors. A high Reynolds number (Re) improves the mixing rate and selectivity of the reactions, but some exceptions of increasing side product yield with the higher Re have been reported. This study investigated the mixing uniformity in microreactors with in-line UV–vis spectroscopy to clarify the relationship between reaction selectivity and chaotic mixing with the higher Re. A colorization experiment of thymolphthalein in an acidic solution was conducted with an excess acid amount to the base to indicate a non-uniformly mixed region. Non-uniformity significantly increased with Re. At the same time, the degree of mixing, which was measured by a usual decolorization experiment, showed that the mixing rate increased with Re. The in-line analysis of the Villermaux–Dushman reaction during the mixing clarified that side product yield significantly increased with Re at around 300 and then decreased at around 1100. These results suggest the compensation effect between the mixing uniformity and mixing rate on the selectivity of the mixing-sensitive reactions. Faster mixing, characterized by a larger Re, can disturb mixing uniformity and, in some cases, decrease reaction selectivity.