The North China leopard population in the eastern Loess Plateau, China, is highly fragmented and faces an increased risk of extinction due to habitat loss and environmental change. Therefore, timely research on leopard conservation in the Loess Plateau region can provide scientific guidance for its management and population recovery. To investigate the impacts of habitat fragmentation on genetic diversity, we analyzed 129 fecal samples from the eastern foot of the Loess Plateau, China. Using eight pairs of microsatellite loci and mitochondrial ND-5 gene sequences, we genetically identified 41 individual leopards. Analysis of microsatellite data showed an intermediate level of genetic diversity (PIC = 0.60). Based on the ND-5 gene sequence, five haplotypes were identified, with a moderate level of genetic diversity (Hd = 0.23, Pi = 0.00048). Inbreeding analyses documented significant population inbreeding pressure. Using VORTEX, we also explored the future development of the population by analyzing the population viability. The results indicated no extinction risk for the leopard population in the next 100 years under current genetic conditions. However, a loss of 22% genetic diversity is expected. These results emphasize the need to strengthen leopard monitoring, mitigate inbreeding, and restore habitat connectivity to preserve genetic diversity.