Abstract: For the uncertainty analysis, the Wilks’ formula was employed to identify the minimum runs and the upper and lower limits of the calculation. An uncertainty analysis method and program for sub-channel code were developed based on the existing uncertainty analysis method. The void fraction predicted by the sub-channel code was compared with the uncertainty limit. The results show that the uncertainty of the side and the corner sub-channel is smaller, which is about ±5.5%; the uncertainty of the sub-channel around the water rod inside the bundle is bigger, which is about ±9%. The uncertainty of high void fraction sub-channels which are the most important sub-channels is about -5.5%-6%.