The invention discloses a device and a method for quickly separately filling thumb tubes with frozen semen in slim tubes. The device comprises a slim tube barrel, a tube insertion base and a vibrationdevice. An opening is formed in the upper end of the slim tube barrel, a plurality of guide tubes are arranged at the bottom of the slim tube barrel, a plurality of insertion holes corresponding to the guide tubes are formed in the tube insertion base, limit devices are arranged at the bottom of the slim tube barrel and on the tube insertion base, the thumb tubes on the insertion holes are connected with the guide tubes when the slim tube barrel is connected with the tube insertion base by the limit devices, and the vibration device is connected with the tube insertion base. The device and the method have the advantages that the thumb tubes can be quickly separately filled with the frozen semen in the slim tubes by the aid of the device and the method, the frozen semen in the slim tubes does not need to be separated from liquid nitrogen in separate filling procedures, the quality of the frozen semen can be improved, the liquid nitrogen contact time of people can be shortened, the workefficiency can be improved, and the device and the method are favorable for the physical health of staffs and have important significance in the technical field of artificial insemination.