<p>The mountainous environment of Nanjing, China, has historically held significant importance. However, many of its mountains today face the challenges of being covered by urban development and the loss of their historical names. To protect these mountains and their names, it is essential to understand their history. However, most historical mountain names found in local gazetteers cannot be directly established to have corresponding relationships with contemporary mountains. This paper used a variety of historical materials and examined the geographical locations of 108 mountains in the core area of Nanjing in the Southern Song Dynasty (1127–1279), categorized into five situations. It created a map of mountain names and distinguished the deviations between ‘cognitive geography’ and ‘real geography’. This paper revealed that in the Southern Song, the perceived mountains formed six distinct distribution belts, forming an inner and an outer layer. Three mountain belts in the inner layer were found to form a Y-shaped structure with the city, creating three types of city-mountain relationships. It also uncovered the reasons for the deviations between the local gazetteer records and the actual geographic situation. These deviations were mainly caused by the scholars’ method of measuring distances along routes, which also contributed to the misplacement of place names in historical maps.</p>