$re = '/((?!#){2}[\s\S])+/';
$str = '## chapter 1
Lorem ipsum dolor sit amet, consectetur adipiscing elit.
Suspendisse mollis magna nec felis gravida, id posuere libero molestie.
### subchapter 1.1
Sed vel ipsum eget tortor maximus ultrices vitae eget dolor.
## chapter 2
Aenean pellentesque lectus quis ex tristique ultrices. Vestibulum eget purus eu ipsum vestibulum pulvinar
';
preg_match_all($re, $str, $matches, PREG_SET_ORDER, 0);
// Print the entire match result
var_dump($matches);
Please keep in mind that these code samples are automatically generated and are not guaranteed to work. If you find any syntax errors, feel free to submit a bug report. For a full regex reference for PHP, please visit: http://php.net/manual/en/ref.pcre.php