The invention discloses a method for detecting risk factors of imported agricultural and forestry animals and plants. The method is implemented on a micro-region image and spectrum integrated detection system. The method comprises five steps of initialization, spectral self-focusing of a current imaging region, spectral signal acquisition, wide spectrum imaging of the current imaging region, scanning wide spectrum detection and imaging, and post-spectrum processing. The invention has the beneficial effects that the supercontinuum laser reflection microscopic imaging and reflection spectrums ofthe risk factors are simultaneously acquired by the image and spectrum integrated method, and the microscopic imaging uses a region splicing method to obtain a high-resolution supercontinuum microscopy image of a larger sample. In addition, the supercontinuum reflectance spectroscopy calculates a mean expected spectrum and a variance spectrum, provides important spectral features of the sample, and provides important support for detection, database construction, traceability and identification.