Which spacecraft carried the first resident ISS crew into orbit?

Soyuz TM-31 carried the first resident ISS crew into orbit.

Launched from Baikonur Cosmodrome on 31 October 2000, Soyuz TM-31 transported Yuri Gidzenko, Sergei Krikalev, and NASA astronaut William Shepherd. After docking with the station, the three became Expedition 1, the first long-duration crew assigned to live aboard the ISS.

The mission marked the start of continuous human occupation of the station. Expedition 1 formally began its residence in November 2000 and spent about four months conducting station maintenance, scientific work, and preparations for future crews. Shepherd commanded the expedition, while Gidzenko and Krikalev served as its Russian cosmonaut members.

This question can cause confusion because several nearby missions also involved the ISS. The uncrewed Progress M1-3 delivered supplies, while STS-102 later rotated the first expedition out and brought Expedition 2 in. Soyuz TMA-1 was a later Soyuz spacecraft, not the vehicle that launched the first resident crew. Soyuz TM-31 was both the first Soyuz mission to dock with the ISS and the crew transport for Expedition 1.