An imaging method that uses multi-layer flat panel detector to acquire X-ray multi-energy images is proposed. Single layer， multi-layer flat panel detector structure is introduced， as well as multi-layer flat panel detector detection imaging system mechanism. X-ray imaging principle is explained， dual energy imaging， subtraction principles are studied by performing single energy X-ray switching simulation with twice shots. Furthermore， different kVp， filters induced X-ray energy spectrum is analyzed， and low， medium， high energy chest phantom images are acquired by performing kVp switching experiment with several shots. Results show that multi-energy images of chest phantom exhibit difference between rib and lung region， and bone enhancement， suppression can be realized by performing dual energy subtract to multi-energy images. Similarly dual energy imaging， subtraction principles are studied by performing dual energy X-ray excited dual layer flat panel detector imaging simulation with single shot. Same kVp with different filter combination induced X-ray energy spectrum is analyzed， multi-layer flat panel detector imaging experiment with single shot is performed， and low， high energy chest phantom images are acquired by first， third layer flat panel detector. Results show that low， high energy images also exhibit difference between rib and lung region， bone enhancement， suppression can also be realized by performing dual energy subtraction. Experiment result proves that X-ray multi-energy imaging using multi-layer flat panel detector detection method is practicable.