Green roofs provide various ecosystem services, including habitats for diverse organisms in urban areas where natural space is very scarce. This study aims to evaluate the restoration effects of green roofs created by applying an ecological restoration method to reinforce habitat function. The reference ecosystem selected for the ecological restoration of a roof was a Korean red pine stand established on Mt. Bulam, considering the soil depth, light, moisture conditions, etc., compared with the roof’s environmental conditions. Ecological restoration was carried out by planting two-year-old pine seedlings and scattering surface soil collected from the pine stands. The pine trees showed geometrical growth in height and diameter and a high water-use efficiency. The ecological restoration of the green roofs demonstrated an ecological function for improving the urban climate through the mitigation of the urban heat island effect and high productivity, showing different functions depending on the greening method. The composition and diversity of vegetation and insects at the ecological restoration site were similar to those at the reference site, whereas the landscape architecture sites, which were created using the landscape architecture method, were different from the reference site. These results confirm that applying the ecological restoration method for rooftop greening resulted in better biological habitat function than applying existing landscape architecture methods.