The invention provides a small-opening bird's nest bottle filling method and a natural filling auxiliary agent. The small-opening bird's nest bottle natural filling auxiliary agent takes a natural filling auxiliary agent prepared from lotus leaf powder, aloe vera gel, pectin, konjac glucomannan and seaweed gel as an auxiliary lubricating agent, the surface of a funnel is coated with the natural filling auxiliary agent, filling is performed, so that the auxiliary agent solves the problem that bird's nests do not easily pass an opening of a small-opening bird's nest bottle as the diameter of the opening is small, vibration or cutting of the bird's nests is decreased, filling efficiency is improved, original strips of the bird's nests are kept, and loss of nutrient components is reduced. According to the small-opening bird's nest bottle filling method, filling time of the bird's nests is saved, and filling efficiency is improved.