您的模型定义不正确,应该如下修复。

// var Schema = mongoose.Schema;
var User = mongoose.model('User',{ 
  email: String, 
  classes: [ {type: Schema.Types.ObjectID, ref: 'Class'}] 
});

var Class1 = new Class({/*yourDataWillBeHere*/})

Class1.save(function(err, classData) {
   var User1 = new User({/*YourDataWillBeHere*/})
   User1.classes.push(classData._id);
   User1.save(function(err, userData) {
      //make something with userData object 
   })
})

populate() 这样地

User
.find()
.populate('classes')
.exec()