Database

db={user_profile:[{"phone_number":"222","primary_skills":[{skill_id:1,years:12},{skill_id:2,years:13}]}],skills:[{id:1,name:"php"},{id:2,name:"java"}]}

Query

db.user_profile.aggregate([{$unwind:"$primary_skills"},{$lookup:{from:"skills",localField:"primary_skills.skill_id",foreignField:"id",as:"primary_skills.name"}},{$unwind:{path:"$primary_skills.name"}},{$addFields:{"primary_skills.name":"$primary_skills.name.name"}},{$group:{_id:"$_id",phone_number:{$first:"$phone_number"},primary_skills:{$push:"$primary_skills"}}}])

Result