Hidden dangers such as cracks, surface concrete denudation and groundwater infiltration appeared on Pandaoling tunnel, a long-distance pressure-free tunnel with a length of 15.723 km due to the complex lithology and severe geological conditions. In September 2013, the tunnel was reinforced with lining of a minimum thickness of 0.25 m which reduced the tunnel’s overflow section. The reinforcement also reduced the roughness of tunnel surface which is a key factor determining whether the overflow capacity meets design requirement. Conventional calculation and test of roughness could hardly meet accuracy requirements. In view of this, prototype observation was conducted. The theoretical basis, observation approaches and methods of prototype observation are introduced in this paper, and the rationality of observed roughness and discharge capacity of tunnel sections are analyzed. The roughness of rectangular open section, tunnel entrance without reinforcement, tunnel entrance with reinforcement, and tunnel outlet with reinforcement is 0.013 07, 0.015 49, 0.011 16, 0.010 52, respectively. According to the measured water level in the observation section, the overflow capacity of the Pandaoling tunnel after reinforcement meets design requirements.