I have 2 cartons each weighing 25 pounds. Carton dimensions are 30" X 18" X 18".

The cheapest way should be the surface mail of China Post, which costs around CNY 300 for a 25 pound parcel.

My factory office is in Hong Kong and they have quoted to me $1000 to ship those two boxes China post. I called Fedex and it is $335 per 25KG box (flat rate) but I cannot fit all pieces into ONE box.

I cannot believe this is so expensive or find an alternative solution.

DHL is expensive too. EMS is even worse! Very hard to find answer from the other side of the world.

There are many shipping agents, they have a discount for ems/DHL shipping.
Google " 'suppliers city' to USA DHL discounts' " and you will find this agemts easily.
I personally had used their service to send 50kg ems to Thai.
Another option is air cargo, usually freight forwarders provide 'air freight ' additionally to 'sea freight'.
Air freight is exactly for not heavy (up to 100kg) parcels.