The Shuanghuaishu (SHS) site in China is one of the 100 most important archaeological discoveries over the past 100 years; its historical heritage can be traced directly back 5300 years. Understanding the early landscape of the site would provide important information about the origin of Chinese civilization. The SHS site is buried and surface traces are difficult to see; therefore, we attempted to reconstruct the early landscape of the site based on a current surface landscape model and environmental archaeological analysis. We created a modern three-dimensional (3D) landscape model of the study area from high spatial resolution unmanned aerial vehicle (UAV) aerial photographs and analysed the distance change between the Yellow River and SHS site in the past 60 years from CORONA and Landsat images. By combining environmental archaeological survey results, archaeological excavation data, relevant papers, and field measurements, we reconstructed the paleotopography of the SHS site during the Yangshao period (7000–5000 aBP). On this basis, 3D natural and human landscapes during the Yangshao period were rebuilt. The results show that (1) Satellite images acquired at different resolutions can provide multiscale spatial information about the site, and high-precision models of current conditions can be quickly generated from UAV aerial photography. (2) From 1960 to 2020, the shortest distance between the SHS site and the Yellow River was approximately 512 m. The location of bedrock on Mang Mountain can be used to infer the early extent of the northern terrace at the site. (3) Environmental archaeology provided information about the palaeoenvironment of the site area. By incorporating spatial information technology and 3D visualization, we can better restore the early landscape of the SHS site. Our work integrates environmental archaeology, field archaeology, and spatial technology, enabling data and modelling support for the visual interpretation of the SHS site.