The transient processes of cooling-down and stratifying an initially homogeneous fluid by natural convection in a vertical circular cylinder have been investigated numerically. The transient flow patterns are identified by the visualization of the transient evolving processes in the cylinder. The results show that vigorous flow activities concentrate mainly in the vertical thermal boundary layer along the sidewall and in the horizontal region which is the lower part of the domain where the cold intrusion flow is embedded. The transient flow patterns at the unsteady and quasi-steady stages are analysed, including the activities of the travelling waves in the vertical thermal boundary layer along the sidewall and the cold intrusions in the horizontal region. A scaling analysis is used to characterize the development of the vertical thermal boundary layer on the sidewall and the stratification in the cylinder. It is found that the numerical solutions agree very well with the scaling results.