Although there are 12 advanced technologies on Deep Space 1, the rest of the spacecraft is composed of current, low-cost components that have been tried and tested on other missions. (The Deep Space 1 flight computer, for instance, is based on that used by Mars Pathfinder and other missions.) This approach was used because the focus of the New Millennium Program is on proving that certain advanced technologies work in space, not on building complete spacecraft representative of those to be used in future missions.

The spacecraft structure is an aluminum space frame based on the three Miniature Seeker Technology Integration (MSTI) spacecraft built by Spectrum Astro, Inc. for the Ballistic Missile Defense Organization. (Spectrum was the primary industrial partner on Deep Space 1.) With most of the components mounted on the exterior of the bus, their accessibility simplified replacement during integration and test.

The total mass of the spacecraft as launch was about 486.3 kg, composed of 373.4 kg dry spacecraft, 31.1 kg of hydrazine, and 81.5 kg of xenon. The spacecraft configuration is shown below.