Our study provides a complete overview of the spatial and temporal characteristics of the pandemic influenza (H1N1-2009) epidemic in mainland China in 2009. The epidemic spanned a large geographic area and presented spatial and temporal heterogeneity in different regions of mainland China. Our analyses of the invasion of pandemic influenza indicated that domestic travel by air and by national highways and freeways and population density contributed to the spread of the epidemic. Lower temperatures and lower relative humidity were climatic factors that facilitated local transmission after correction for the effects of school summer vacation and public holidays, as well as population density and the density of medical facilities. The density of medical facilities could have influenced pandemic influenza patient reporting, and this effect seemed more important for the reporting of local transmission (a highly significant positive association) than for reporting of the invasion (borderline significance). This indicates that the CISDCP can be further improved.