Wild tomato species Solanum pimpinellifolium possesses rich variation in many elite characters. In this paper, we analyzed the phenotypic and genetic diversity of 433 genetic resources of S. pimpinellifolium collected from different resource center of the world. The results of phenotyping indicated that about 14% of these accessions are Solanum lycopersicum var. cerasiforme. Among 370 accessions of typical S. pimpinellifolium, about 22% of them are segregated on certain degree. Population variation analysis showed that variation coefficient varied among different traits. The maximum variation existed in stigma and is about 56.716%, while the minimum one is petals number with about 2.082%. Correlation analysis of different traits showed that there is significant correlation between different traits. Based on the data of phenotyping and genotyping, S. pimpinellifolium population were divided into two groups. Principal component analysis further showed that fruiting rate, fruit weight and soluble solids content makes great contribution to the variation. The obtained results may provide the basis for tomato genetic improvement by Solanum lycopersicum.