Microreactor is capable of intensifying catalytic reaction processes. The fabricating of catalytic film inside microchannels for catalytic reaction remains a challenge. Here we report a facile method for in situ fabrication of layered double hydroxide (LDH) film immobilizing gold nanoparticles in capillary microreactor. Through adjusting the reaction condition of in situ hydrothermal crystallization process and flow deposition process inside microchannel, film thickness, film morphology and Au loading of Au/LDH coating can be finely controlled. Such Au/LDH film inside microchannel exhibited good performance in catalytic carbonylation of glycerol with urea. The yield of glycerol carbonate reached 31.9% at flow rate of 10 µl/min, residence time of 6.62 min and reaction temperature of 413 K under atmospheric pressure. The maximum productivity of 3.78 g∙h−1⋅g−1 was obtained at flow rate of 40 µl/min and residence time of 1.65 min under same reaction temperature and pressure. Continuously running the microreactor for 30 h proved the high stability of this catalytic film inside microchannels. This approach could be extended to fabricate other diatomic and triatomic metal LDH films immobilizing metal nanoparticles inside microchannels for heterogeneous catalysis.