The invention discloses a sample conveying system applied to a vacuum interconnection system. The sample conveying system applied to the vacuum interconnection system comprises a vacuum pipeline, at least two sample supports, two vacuum lifting tables corresponding to the at least two sample supports, at least one full-mechanical drive manipulator, at least one sample manipulator, and at least twovacuum magnetic rods. The full-mechanical drive manipulator is at least used for conveying a sample between the sample supports and driving an upper surface and a lower surface of the sample to overturn; the sample manipulator is at least used for fetching and sending the sample in the sample support to a corresponding device; and the two vacuum magnetic rods are used for driving the full-mechanical drive manipulator and the spoon-shaped sample manipulator. By adopting full-mechanical movement in vacuum, the sample is conveyed from one sample support to the other sample support or the device,and the upper surface and the lower surface of the sample are overturned; and in vacuum, an electric or pneumatic servo drive sample conveying process is not adopted, so that a vacuum degree and thecleanliness of the whole system are not influenced, and the sample conveying system applied to the vacuum interconnection system can adapt to a local high temperature working condition and a space dimension in the vacuum interconnection system.