By adding another array
$args = array(
'post_type' => 'custom_post_type',
'meta_query' => array(
array(
'key' => 'size',
'value' => 'big',
'compare' => 'LIKE',
),
array(
'key' => 'gender',
'value' => 'male',
),
)
);
$query = new WP_Query( $args );