The invention relates to an downhole fluid stratified sampling system and a stratified sampling method. The system comprises a downhole tool structure and a ground structure; the downhole tool structure comprises a guiding part, the guiding part is connected with a magnetic positioning short section through a control loop short section, the magnetic positioning short section is connected with a first packer, the first packer is connected with a first cable laying pipe, the first cable laying pipe is connected with an electric control sampling barrel structure in series, a barrel body center channel and at least one sampling channel are formed in the electric control sampling barrel structure, an inlet of the sampling channel corresponds to a sampling layer, the first cable laying pipe is connected with a second packer, the second packer is connected with a pump set, the pump set communicates with a second cable laying pipe, and the magnetic positioning short section, the first packer, the first cable laying pipe, the electric control sampling barrel structure, the second packer, the pump set and the second cable laying pipe are electrically connected through electric and hydraulic quick connectors. According to the downhole fluid stratified sampling system, multi-layer sampling can be rapidly and economically achieved through one-time tubular column, the layered sampling efficiency of downhole fluid is improved, the downhole fluid stratified sampling system is suitable for various well types, reliability is improved, and cost is reduced.