The invention discloses a vacuum sample transfer device which comprises a vacuum cavity, a vacuum pipeline, a magnetic rod, a sample transfer rod and a sample cup, wherein the vacuum pipeline is used for connecting the vacuum cavity and sampling or sample-receiving equipment together; a vacuum valve is arranged on the vacuum pipeline; the magnetic rod comprises a vacuum outer magnetic ring and a vacuum inner magnetic ring; the vacuum outer magnetic ring is located out of the vacuum cavity; the vacuum inner magnetic ring is located in the vacuum cavity; the sample transfer rod is arranged in the vacuum cavity and is connected with the vacuum inner magnetic ring; a Y-shaped sample cup clamp with two branches is arranged at the front end of the sample transfer rod; the sample cup is used for loading a vacuum sample, is of a concave step structure, and is assembled on the sample transfer rod by virtue of the clamping matching between the concave step structure and the two branches; through the design of the Y-shaped sample cup clamp at the front end of the sample transfer rod and the concave step structure of the sample cup, the vacuum sample is stable and reliable in the transferring process; the problem that the sample falls off is not caused; and the vacuum sample transfer device disclosed by the invention is simple in structure, low in cost, and high in universality, and can be applicable to sample chambers and sample stages of different vacuum systems.