The present invention relates to a nucleic acid hybridization method and in particular to a method using a microfluidic chip-based hybridization device with modified procedures which shows the advantages of simplicity and efficiency. The method of the present invention is to mix the test nucleic acid and the probe nucleic acid in advance, feed the solution into a hybridization device with a porous substrate, let the nucleic acid to be analyzed absorb into the substrate. The washing solution is then injected into the same device to wash out the unhybridized probes and the signals of hybridization absorbed on the substrate are detected for analysis. The conventional 2-step approach for the hybridization of the nucleic acid to be analyzed and the probe is combined into one step by the method of the invention provided here, which simplifies the necessary steps and shorten the time needed for hybridization reaction and detection.