As the historical and contemporary values of Chinese traditional villages continue to emerge and the circumstances of the times change, their preservation has a lasting and far-reaching significance in promoting the revitalisation and sustainable development of China’s countryside. However, rapid urbanization began after China’s reform and opening up, and continuous urban expansion led to the rapid decline or even disappearance of these villages. Previous studies on village protection tend to focus on morphological studies from the perspective of individual units, and rarely discuss the influencing factors of spatial distribution. Therefore, there are certain deficiencies in revealing the distribution rules, which makes it difficult to fully carry out the protection work. The article reconstructs the traditional village system of Fujian Province, whose traditional villages cover both national and provincial historical and cultural villages and national and provincial traditional villages. The spatial distribution characteristics and influencing factors of traditional villages in Fujian Province were studied using 1,606 traditional villages of various levels as research objects. The results of the study show that: (1) the spatial distribution of traditional villages in Fujian Province is cohesive, with significant uneven distribution, and there are three high-density agglomerations and two sub-density agglomerations; (2) The spatial distribution shows a pattern of “large scattering, small concentration, more in mountainous areas and less in coastal areas”; (3) Topography, river systems, transportation and socio-economic conditions combine to influence the spatial distribution of traditional villages in Fujian Province, but the degree of influence varies. Physical and geographical conditions play a leading role in the distribution of traditional villages, and road traffic conditions and socio-economic conditions have a secondary impact on the distribution of traditional villages. There is an obvious agglomeration of traditional villages in the mountainous river areas, while there is a certain degree of negative correlation between road traffic conditions and socio-economic conditions and the number of traditional villages. (4) With the support of good policies and economic conditions, the protection and continuation of traditional villages can be promoted to a certain extent, and it is also conducive to the spread of local multicultural culture. Finally, corresponding policy recommendations are made for the conservation and sustainable development of traditional villages in Fujian Province.