To obtain high performance CH3NH3PbI3 perovskite solar cells, it is highly important to realise a high open-circuit voltage. Calculation results based on a modified diode model have indicated that a low bare ratio ϕ of the perovskite film is the most important factor determining the open-circuit voltage, where ϕ is defined as the ratio of the projection of the uncovered area of the perovskite film to the apparent area of the total substrate surface. To realise a low ϕ, we investigate the nucleation behaviour of crystals on rough substrates. The analysis results predict that, when CH3NH3PbI3 is deposited on conventional transparent conductive oxide substrates such as fluorine-doped tin oxide, preferential heterogeneous nucleation will occur on the concave regions of the substrate; then, depending on the subsequent growth step, full coverage of the perovskite film at both the macroscopic and microscopic scales is realised. As a result, an ultra-high open-circuit voltage, i.e., 1.20 V, can be achieved in devices using the full coverage CH3NH3PbI3 film. The thermodynamics theory of precipitation nucleation should shed light on solution engineering of thin films.