经过30分钟的研究，我得出了以下解决方案：

function wpse_175564() {

  // The html goodies with shortcodes
       $htmlcodes = \'<div class="akismet_activate">
                <div class="aa_a">A</div>
                <div onclick="document.akismet_activate.submit();" class="aa_button_container">

            [the_shortcode id="4"]

            <div class="aa_button_border">
                <div class="aa_button">Activate your Akismet account</div>
                </div>
                </div>
                <div class="aa_description"><strong>Almost done</strong>
     - [the_shortcode id="4"] activate your account and say goodbye to comment spam</div>
                </div>\';
         // End of HTML Goodies

               // Let\'s get the shortcode inside the string and execute it!

                $pattern = get_shortcode_regex();
  if (preg_match_all( \'/\'. $pattern .\'/s\', $htmlcodes, $matches ) && array_key_exists( 2, $matches )) {

       foreach($matches[0] as $i => $v){
          $htmlcodes = preg_replace($v , do_shortcode($v), $htmlcodes);
          $htmlcodes =  str_replace(array(\'[\',\']\'), \'\', $htmlcodes);
         }


  } 

 return $htmlcodes;

}

如果要直接在php模板中插入短代码，必须使用do_shortcode().

例如：

<?php echo do_shortcode( \'[the_shortcode id="4"]\' ); ?>