Wind-induced vibration related fatigue analysis of a long-span lattice structure was performed both in the time and frequency domains based on the multiple point pressure measurement wind tunnel test data according to the Miner’s linear cumulative damage theory in order to analyze the wind-induced fatigue damage of long span lattice structures under wind load. Four methods were applied for estimating wind-induced damage on the structure, i.e., the time domain rain-flow method, the equivalent stress method, the equivalent narrow band method and the equivalent wide band method. The influences of the joint distribution of wind speed and direction on the fatigue damage of the structure were carefully assessed by constructing the joint probabilistic distribution function. The wind-induced fatigue damage of spherical joints in the steel lattice structure was evaluated with the empirical formula of high-strength bolt stresses. Results show that the equivalent wide band method is a more accurate method for fatigue damage calculation in frequency domain. The fatigue damage of the lattice structure is more likely to occur under the wind directions of 40°~60° compared with other wind direction angles. The cumulative fatigue damage of spherical joints is more significant than that of the structural members themselves considering the joint distribution of wind speed and direction.