Dear Peng,
The Pajek format is a bit problematic as there exists no formal specification for it so we don't know what is the "official" way to store any arbitrary vertex or edge attributes in this format.
To complicate matters further, the Pajek file also contains visualization-related data (e.g. vertex color, font size, edge widths etc). igraph_read_graph_pajek() processes these and then converts them to vertex / edge attributes with more meaningful names; see this page for more details:
igraph_write_graph_pajek() recognizes these attributes only and converts them back to the appropriate fields in the Pajek output.
If storing vertex / edge attributes is important to you, I advise you to use a more formalized graph format such as GraphML if that's possible in your project.
Also, please note that the igraph-help mailing list is about to shut down soon. The discussion forums have been moved to Discourse at
https://igraph.discourse.group -- you are more likely to get responses there than on the mailing list.
All the best,