In autumn of 1945, after won the victory in war with Japanese, when Taiwan and Pen-Hu returns to the Republic of China, Navy of R.O.C. received one mission, it is to receive the Ce-Tian Island Base of Japanese Army, in December R.O.C. Navy found a Navy branch office and a shipyard in Pen-Hu. In April, 1948 the Navy reorganize and consolidate the Navy branch office to be a Patrol and Defense Section grade "A".
In May of 1950 the Navy cancel the Patrol and Defense Section change to be Pon-Hu Alert Harbor Command Department, and in May 16th, 1955 changed be Second Base Command Department. In July of 1998 Navy canceled the Second Base Command Department. In the past the base is Japanese factories, this place changed be R.O.C. Navy Makung Shipyard, in July of 1949, the Navy take in workers of Shanghai, Putong, Daku, Mawei, workers and some equipments come from China and come here to Pen-Hu, and enlarge it be Navy Second Shipyard, follow it in May of 1957, named be Navy Second Shipyard Factory, July of 1999 change be Navy Makung Shipyard Factory. In March 16th, 2000, R.O.C Army have a new program to reduce and reorganize the Army to be more strong and powerful, Navy Second Shipyard take over the Second Factory Base with administration and logistic support service, they transform it by Factory to Base, to united "Defense Base" and "Logistic Support" power, and named be Navy Makung Logistic Support Command Department. In October 1st, 2002, the commander official rank changes lower to Captain.
Emblem：
- The feature of the logo is a shield .It represents to protect the country .
- The inner distinguish four blocks .It represents to overrun the four seas for navy .
- The ship represents to brave the wind and waves .
- The rice stalk and an anchor represent to shoulder the duty of the logistics support of navy .
- The inner logo of an anchor is a transfiguration of calligraghy of "Makung Logistic"，and represents to welcome 2000 A.D .