How to Programmatically set a Product's Multi-Select Attribute by Labels
Multiselect attributes can be set as a comma separated list (or also an array) containing the attribute value ids.
So first we have to convert the actual values to Magento's internal ids.
$attrCode = 'color_base';
$sourceModel = Mage::getModel('catalog/product')->getResource()
->getAttribute($attrCode)->getSource();
$valuesText = explode(',', 'red,green,blue');
$valuesIds = array_map(array($sourceModel, 'getOptionId'), $valuesText);
$product->setData($attrCode, $valuesIds);
$product->save();
Modify last line of the above code
$product->save();
with
$product->getResource()->saveAttribute($product, $attrCode);
It works