In the past, a great deal of research has been conducted to determine the fractal properties of river networks, and there are many kinds of methods calculating their fractal dimensions. In this paper, we compare two most common methods: one is geomorphic fractal dimension obtained from the bifurcation ratio and the stream length ratio, and the other is box-counting method. Firstly, synthetic fractal trees are used to explain the role of the junction angle on the relation between two kinds of fractal dimensions. The obtained relationship curves indicate that box-counting dimension is decreasing with the increase of the junction angle when geomorphic fractal dimension keeps constant. This relationship presents continuous and smooth convex curves with junction angle from 60° to 120° and concave curves from 30° to 45°. Then 70 river networks in China are investigated in terms of their two kinds of fractal dimensions. The results confirm the fractal structure of river networks. Geomorphic fractal dimensions of river networks are larger than box-counting dimensions and there is no obvious relationship between these two kinds of fractal dimensions. Relatively good non-linear relationships between geomorphic fractal dimensions and box-counting dimensions are obtained by considering the role of the junction angle.