The invention belongs to the field of petroleum engineering, and concretely relates to an experiment apparatus for measuring the permeability of a low permeation rock core, and a method thereof. The apparatus for measuring the permeability of the low permeation rock core comprises an inlet end pressure cap, an outlet end pressure cap, a curing glue sleeve, a carbon oxide gas bottle, a glass funnel, a first scale, a vacuum pump, a polyfluortetraethylene pipe and a second scale, and three ports of a first tee joint are respectively connected with the outlet of the inlet end pressure cap, the carbon dioxide gas bottle and the glass funnel through pipelines and valves; the glass funnel is vertically arranged, and one side of the glass funnel is vertically provided with the first scale; and three ports of a second tee joint are respectively connected with the outlet of the outlet end pressure cap, the vacuum pump and the polyfluortetraethylene pipe through pipelines and valves, the polyfluortetraethylene pipe is horizontally fixed, the polyfluortetraethylene pipe, a tested rock core and the axis of the first tee joint are in a same horizontal line, and one side of the polyfluortetraethylene pipe is provided with the second scale in a parallel manner. The experiment apparatus for measuring the permeability of the low permeation rock core has the advantages of small dead volume and high metering precision.