I found a way to return the data as I wish, by using aggregate with $unwind.
Cities.aggregate([{
$unwind: '$states'
},
{
$unwind: '$states.cities'
},
{
$match: {
'states.cities.name': {$regex: city, $options: "i"}
}
}
],
function (error, data) {
return res.json(data);
})
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