The invention relates to a micro-fluidic gene detection chip which comprises a sample adding cell, a sample separation element and a detection element, wherein the detection element comprises a detection cell loaded with a bacterial detection agent, a detection cell loaded with a Rickettsia detection agent, a detection cell loaded with a virus detection agent, a detection cell loaded with a fungusdetection agent and a detection cell loaded with a biotoxin detection agent. Multiple types of pathogenic microorganisms can be simultaneously detected during each sample loading, the sample treatment step is simple, and the detection efficiency is high. Meanwhile, the sample addition amount is easily controlled, the volume of to-be-detected liquid entering each detection cell is the same, the detection result is accurate, and the application requirements for rapidly detecting and troubleshooting pathogenic microorganisms at high efficiency and large sample amount during port health quarantine can be met.