After the UN took control of Macross Island, a military base of operations was built to secure the area and begin the immense task of studying the derelict alien battlefortress. This base eventually grew into Macross City, housing a population of thousands of engineers, military personnel and civilian families who were associated with the SDF-1 reconstruction project.
Macross City, along with the rest of Macross Island, was accidentally transported to Pluto orbit when the SDF-1's spacefold system malfunctioned. Much of the city was salvaged and reconstucted inside the hull of the SDF-1, and this internal city was also known as Macross City afterwards.
After the first Robotech War came to an end, the SDF-1 landed at its final resting place in North America. The survivors of Macross City began to recolonize the area and built the City of New Macross around the SDF-1.