In this study, the pH-response of the zwitterionic polydopamine layer to the palladium deposition in a capillary microchannel and the resultant catalytic performance for the nitrobenzene hydrogenation were explored. Experimental results showed that the polydoapmine layer exhibited the switchable surface charge from positive to negative with increasing the pH value. Under low K2PdCl4 concentration, the intrinsic low pH not only allowed most palladium to be deposited at the inlet region of the microchannel, but also provided more accessible sites for the anion PdCl42- deposition. Such property resulted in less palladium deposited at the outlet region because of the limited supply of the precursor and poor mass transfer, while an excellent size distribution of the deposited palladium nanoparticles at both the inlet and outlet of the microreactor was obtained. With the increase of the K2PdCl4 concentration, the increased pH value of the precursor solution aggravated the dispersity of the deposited palladium species and led to large palladium particles at the upstream of the microreactor. The gradually lowered pH value of the precursor solution along the microchannel and the large concentration gradient could directly intensify the anion PdCl42- deposition. Thus, an inverse palladium distribution between the inlet and outlet regions was observed due to the shift of surface potential from negative to positive along the microchannel. Such feature influenced both the catalytic activity and the durability for the nitrobenzene hydrogenation. The obtained results in this work are beneficial for not only the controllable metal catalyst preparation but also the improvement in the economy utilization of catalyst.