Global Navigation Satellite System (GNSS) troposphere tomography has become one of the most cost-effective means to obtain three-dimensional (3-d) image of the tropospheric water vapour field. Traditional methods divide the tomography area into a number of 3-d voxels and assume that the water vapour density at any voxel is a constant during the given period. However, such behaviour breaks the spatial continuity of water vapour density in a horizontal direction and the number of unknown parameters needing to be estimated is very large. This is the focus of the paper, which tries to reconstruct the water vapor field using the tomographic technique without imposing empirical horizontal and vertical constraints. The proposed approach introduces the layered functional model in each layer vertically and only an a priori constraint is imposed for the water vapor information at the location of the radiosonde station. The elevation angle mask of 30° is determined according to the distribution of intersections between the satellite rays and different layers, which avoids the impact of ray bending and the error in slant water vapor (SWV) at low elevation angles on the tomographic result. Additionally, an optimal weighting strategy is applied to the established tomographic model to obtain a reasonable result. The tomographic experiment is performed using Global Positioning System (GPS) data of 12 receivers derived from the Satellite Positioning Reference Station Network (SatRef) in Hong Kong. The quality of the established tomographic model is validated under different weather conditions and compared with the conventional tomography method using 31-day data, respectively. The numerical result shows that the proposed method is applicable and superior to the traditional one. Comparisons of integrated water vapour (IWV) of the proposed method with that derived from radiosonde and European Centre for Medium-Range Weather Forecasts (ECMWF) ERA-Interim data show that the root mean square (RMS)/Bias of their differences are 3.2/−0.8 mm and 3.3/−1.7 mm, respectively, while the values of traditional method are 5.1/−3.9 mm and 6.3/−5.9 mm, respectively. Furthermore, the water vapour density profiles are also compared with radiosonde and ECMWF data, and the values of RMS/Bias error for the proposed method are 0.88/0.06 g/m3 and 0.92/−0.08 g/m3, respectively, while the values of the traditional method are 1.33/0.38 g/m3 and 1.59/0.40 g/m3, respectively.