Rapid urbanization is causing changes in green spaces and ecological connectivity. So far, urban ecosystem research has mainly focused on using landscape metrics (LM) in two-dimensional (2D) space. Our study proposes three-dimensional (3D) measures of urban forests (UF) and LM calculations using LiDAR technology. First, we estimated the UF volume of Krakow (Poland) and the distribution of vegetation (low, medium, high) using a voxel-based GEOBIA approach based on the ALS LiDAR point cloud, satellite imagery, and aerial orthophotos at specific timestamps: 2006, 2012, 2017. Then, the appropriate landscape metrics were selected (NP, AREA_MN, CONTIG_MN, LPI, PARA_MN, SPLIT, MESH, PD, DIVISION, LSI) to quantify the differences between the 2D- and 3D-derived vegetation structures and detect changes in the urban landscape. The results showed that areas with low vegetation decreased due to the expansion of built-up areas, while areas with medium and high vegetation increased in Krakow between 2006, 2012, and 2017. We have shown that the lack of information on the vertical features of vegetation, i.e., 2D greenery analysis, leads to an overestimation of landscape connectivity. In the 3D vegetation classes, it was observed that low vegetation was the best connected, followed by high vegetation, while medium vegetation was dispersed in the city space. These results are particularly relevant for the urban environment, where the distribution of green space is crucial for the provision of ecosystem services.