I have found a way to solve it - that is to write once before save and rewrite. But I don't feel like this is the proper way to do it, can anyone advise me on this? Thanks.

....
$Event = new Event();               
if ($EventID == 0) {      
$Event->write(); //write the event once before save would solve the problem
} else {
$Event->ID = $EventID;
}

$form->saveInto($Event);
$Event->write();      
...

The code is at the Page controller where you add your object, you may check out the structure of the codes in silverstripe tutorial http://doc.silverstripe.org/framework/en/tutorials/3-forms, my codes is as shown below:

class EventAddPage_Controller extends Page_Controller
{
...
public function doFrontEndForm($data, $form)
{

         $Event = new Event();                     
         $Event->write(); //for adding new record, it will have error when it comes to many-many relations if without write once   before save
                              
         $form->saveInto($Event);
         $Event->write();   
}
...
}