I cannot change the font size of package explorer in Eclipse

On Juno and up you can adjust that font by CSS.

Lookup the files in eclipse\plugins\org.eclipse.platform_4.2.x.y\css for your current style sheet (probably e4_default_win7.css), and then just add the following rule:

#org-eclipse-jdt-ui-PackageExplorer Tree,
#org-eclipse-ui-navigator-ProjectExplorer Tree {
  font-size: 10px; /* <-- Desired font size */
}

Update: stylesheets are in eclipse/plugins/org.eclipse.ui.themes_x.x.x.vxxxxx/css folder since Eclipse 4.4 (Luna).

FYI:

From Eclipse v4.4 (Luna):

It looks like the CSS files are no longer in the old folder:

`eclipse/plugins/org.eclipse.platform_4.x.x.vy/css`,

They are moved to the new folder:

eclipse/plugins/org.eclipse.ui.themes_x.x.x.vxxxxx/css

And you must select a theme to apply it, in the menu Windows → Preference → General → Appearance.