Google explained "site: operator and Sitemap" stats

The difference between the number of indexed results of site: operator and Sitemaps report in Webmaster Tools is because Sitemap report only reflects the URLs you've submitted. While the site operator takes into account whatever Google has crawled, which may include newly added URLs or other URLs discovered via links. “Your Sitemap report provides more granular statistics about the URLs you […]

The difference between the number of indexed results of site: operator and Sitemaps report in Webmaster Tools is because Sitemap report only reflects the URLs you've submitted. While the site operator takes into account whatever Google has crawled, which may include newly added URLs or other URLs discovered via links.

“Your Sitemap report provides more granular statistics about the URLs you submitted, such as the number of indexed URLs vs. the number submitted for crawling, and Sitemap-specific warnings or errors that may have occurred when Google tried to access your URLs,” eplain Search Quality Team.