Database
[{"_id":ObjectId("5a934e000102030405000000"),"name":"a","user":ObjectId("5a934e000102030405000001")},{"_id":ObjectId("5a934e000102030405000002"),"name":"a","user":ObjectId("5a934e000102030405000001")},{"_id":ObjectId("5a934e000102030405000003"),"name":"b","user":ObjectId("5a934e000102030405000001")},{"_id":ObjectId("5a934e000102030405000004"),"name":"a","user":ObjectId("5a934e000102030405000005")}]
Query
db.collection.aggregate([{$group:{_id:{name:"$name",user:"$user"},doc:{$first:"$$ROOT"}}},{$replaceRoot:{newRoot:"$doc"}},{$merge:{into:"collection"}}])