Understanding the mechanisms that shape the geographic distribution of plant species is a central theme of biogeography. Although seed mass, seed dispersal mode and phylogeny have long been suspected to affect species distribution, the link between the sources of variation of these attributes and their joint effects to the distribution of seed plants remain poorly documented. This study aims to quantify the joint effects of key seed traits and phylogeny on the species' distribution. We collected seed mass and seed dispersal mode from 1,616 species of seed plants representing 554 genera of 130 families. We used 5,639,009 specimens to calculate species range size through ArcGIS10.2. Phylogenetic generalized least squares regression modeling and variation partitioning were performed to estimate the joint effects of seed mass, seed dispersal mode and phylogeny on species distribution. We found that species range size was constrained by seed dispersal mode and phylogeny. Seed mass and its intraspecific variation were also important in limiting species distribution, but their effects were different among species with different dispersal modes. Variation partitioning revealed that seed mass, seed mass variability, seed dispersal mode and phylogeny together explained 40.44 % of the variance in species range size. Seed traits are not typically used to model the geographic distributions of seed plants. This study provides direct evidence that seed mass, seed dispersal modes and phylogeny explain species distribution variation on a large geographic scale. Our findings underscore the necessity to include seed traits and the phylogenetic history of species, together with existing climate-based niche models, in predicting the response of plant geographic distribution to climate change.