Two-dimensional (2D) layered black phosphorus (BP), with a direct band gap and high carrier mobility, has shown great potential for next generation electronics and optoelectronics. However, 2D materials always show different thermal properties when compared to its bulk counterpart. Therefore, it is necessary to understand the thermal process of BP to reveal its natural physical properties. Herein, an atomic-scale microscopic and spectroscopic study is performed to characterize the thermal degradation and re-deposition of solution-exfoliated BP. The in situ decomposition temperature of the BP is observed to be greater than 400 °C. The residual gaseous BP would be re-deposited to form amorphous phosphorus when the chamber was cooled down to room temperature. Moreover, the thickness of the BP flakes can be moderately controlled through thermal thinning process. Our study provides an insight into the thermal stability of 2D BP in vacuum and opens an avenue in fabricating large-area ultra-thin BP films.