There is a way to do this. Let me try to see if I can put it into words. Look at the stylesheet mentioned above (../wp-includes/js/thickbox/thickbox.css) and use it for reference as to which class you need to update.
Then in your custom theme css style copy and paste or retype the class you want to tweak (this way your customization won’t get overwritten on an update). Now to get the class in your theme stylesheet to take hierarchy, you need to make the classes super specific.
Example1: The thickbox window has a default background of white (#FFFFFF), I want to change it to grey (#CCCCCC). So, I find the class name from thickbox.css which is
`#TB_window {
background:#FFFFFF;
…
}`
In my theme stylesheet, I add
`div#TB_window {
background-color:#CCCCCC;
}</blockquote>`
This kind of “tricks” the CSS, the more specific style reference takes trump.
Example2: Up the caption size to 20px, make it orange and italic
thickbox.css:
`#TB_caption{
height:25px;
padding:7px 30px 10px 25px;
float:left;
}`
My custom stylesheet.css:
`#TB_window #TB_caption {
font-size:20px;
color:#f95000;
font-style:italic;
}`
I hope this makes sense!