The invention discloses a direct imaging method for spiral discrete scanning type fluorescent agent pharmacokinetic parameters. The direct imaging method includes the steps that fluorescent agent scanning data is obtained according to a three-dimensional spiral discrete scanning mode, a multi-mesooecium fluorescent agent kinetic model and a pharmacokinetic parameter direct imaging state equation are set up, a pharmacokinetic parameter image is obtained based on self-adaption extended Kalman filtering, the mesooecium concentration and middle vector are obtained through an obtained final estimated value of the state vector, and finally the penetration rate and the excretion rate are obtained. The method has the advantages that complete data is not needed in each step of an algorithm, the real-time measurement data is obtained in a spiral discrete scanning mode, and the requirement for high time resolution of data collection equipment is reduced; an organizer is described more accurately through the multi-mesooecium kinetic model, and corresponding physiological significance is achieved; median concentration reconstruction errors of an indirect method are avoided; the influence caused by system original state priori knowledge deficiency is eliminated by self-adaptation extended Kalman filtering.