Well... you just need to construct url at run time. Refer the below code:
string strPopup = "YourPopupPage.aspx?yourParameterName=" + Server.UrlEncode(paramValue) + "&secondPraramName=" + Server.UrlEncode(paramValue);
Page.RegisterStartupScript("load", "<script type=\"text/javascript\">\n" + "window.open('" + strPopup + "','ApplicationName',config='left=400, top=400, height=200, width=650, status=yes, resizable= no, scrollbars= no, toolbar= no,location= no, menubar= no');\n" + "</script>");