我參考了這篇
Using the window.close method

用我的 Android 試過是可以關閉的

還是你的狀況是發生在 iPhone, WindowPhone or... ?!

<pre class="c" name="code">
<SCRIPT language="JavaScript1.2">
function popuponclick()
{
my_window = window.open("",
  "mywindow","status=1,width=350,height=150");
my_window.document.write('<H1>The Popup Window</H1>');  
my_window.document.write('<A href="javascript: window.close();">Close the Popup Window</A>');  
}

function closepopup()
{
	if(false == my_window.closed)
	{
	my_window.close();
	}
	else
	
	{
	alert('Window already closed!');
	}
}
</SCRIPT>

<P>
<A href="javascript: popuponclick()">Open Popup Window</A>
</P>
<P>
<A href="javascript: closepopup()">Close the Popup Window</A>
</P>

若是firefox請參考這裡的說明～
http://www.jb51.net/article/17714.htm