The invention provides a full-automatic and high-throughput micro-fluidic chip system and method for detecting pesticide residue, used for field detection of pesticide residue based on enzyme inhibition reaction. The full-automatic and high-throughput micro-fluidic chip system is mainly composed of a portable analytical detector and a disposable micro-fluidic chip; the plastic polymer material of the micro-fluidic chip is manufactured through existing micro-machining technology; the micro-fluidic chip is composed of a central clamping groove, an extraction chamber, a sample chamber, a reaction chamber, a detection chamber, a micro-groove, a micro-hole and a quality control bar code; reagents (comprising an extracting solution, enzyme, a colour developing agent and the like) required for detecting pesticide residue are fixed in the micro-fluidic chip; the functions of sampling automatically and quantitatively, distributing a fluid, carrying out biochemical reaction and molecular recognition and the like can be realized; a fluid operation and control module, a photoelectric detection module, a data analyzing and processing module and an information storage and communication module are integrated in the portable analytical detector; operation and control of biochemical reaction in the micro-fluidic chip and rapid analysis and detection of to-be-detected indexes and pesticide residue can be realized; and thus, the micro-fluidic chip system and the method provided by the invention are particularly applied to full-automatic and high-throughput detecting and screening of pesticide residue in the samples, such as fruits, vegetables, soil and water.