We present a large catalogue of molecular clouds with accurate distance estimates in the Southern sky. Based on the three-dimensional dust extinction map and the best-fitting extinction and distance information of over 17 million stars presented in Guo et al. (2021ApJ...906...47G), we have identified 250 dust/molecular clouds in the Southern sky using a hierarchical structure identification algorithm. Amongst these are 71 clouds located at high Galactic latitudes (b < -10{deg}). We have estimated the distances to the clouds by fitting the extinction versus distance profiles of the lines of sight overlapping with the clouds, using a simple Gaussian dust distribution model. The typical uncertainties of the distances are less than 7 per cent. We also provide the physical properties of the individual clouds, including the linear radius, mass and surface mass density.