The spatial distribution of heavy metals in the sediments of mountainous rivers is influenced by population density and industry type. In December 2019, sediment samples were collected in a typical mountainous river (Taohuaxi River) which covered both urban and rural sections in Changshou District, Chongqing. The contents of heavy metals in the sediment samples at each point were measured. The results showed that the average heavy metal contents in the sediments of the urban section of Taohuaxi River were higher than those in the rural section for all the eight heavy metals monitored, with significant differences observed in Cd and Cu contents. Human population density was found to affect the spatial distribution of heavy metals in river sediments. A proportion of 20.59% in the monitored sites in the basin was found to be Near Moderate or Moderate Pollution according to the improved Geoaccumulation Index (I_m), indicating that heavy metals were only enriched at certain sites in Taohuaxi River. According to the Potential Ecological Risk Index (RI), 67.65% in the monitored sites in the basin were at Medium or High potential ecological risk. In the Sediment Quality Guideline method (SQGs), the toxicity of heavy metals in the sediments at all monitoring points was found to be of moderate risk to organisms. The ecological risks of heavy metals in the sediments of Taohuaxi River should not be ignored. The results of the Positive Matrix Factorization (PMF) model analysis showed that five main sources of heavy metals in the sediments of Taohuaxi River were identified. The contribution of these sources was in the order of aquaculture sources (38.79%) > natural sources (20.40%) > anthropogenic mixed sources (20.35%) > industrial sources Type II (16.69%) > industrial sources Type I (3.78%).