The piece is divided into nine sections played with only three definite pauses. Strauss named the sections after selected chapters of the book:
  1. (Introduction, or Sunrise)
  2. (Of Those in)
  3. (Of the Great Longing)
  4. (Of Joys and Passions)
  5. (The Song of the Grave)
  6. (Of Science and Learning)
  7. (The Convalescent)
  8. (The Dance Song)
  9. (Song of the Night Wanderer)
The piece starts with a sustained double low C on the double basses, contrabassoon and organ. This transforms into the brass fanfare of the Introduction and introduces the "dawn" motif (from "Zarathustra's Prologue", the text of which is included in the printed score) that is common throughout the work: the motif includes three notes, in intervals of a fifth and octave, as C–G–C (known also as the Nature-motif). On its first appearance, the motif is a part of the first five notes of the natural overtone series: octave, octave and fifth, two octaves, two octaves and major third (played as part of a C major chord with the third doubled). The major third is immediately changed to a minor third, which is the first note played in the work (E flat) that is not part of the overtone series. "Of Those in Backwaters" (or "Of the Forest Dwellers") begins with cellos, double-basses and organ pedal before changing into a lyrical passage for the entire section. The next two sections, "Of the Great Yearning" and "Of Joys and Passions", both introduce motifs that are more chromatic in nature. "Of Science" features an unusual fugue beginning in the double-basses and cellos, which consists of all twelve notes of the chromatic scale. It is one of the very few sections in the orchestral literature where the basses must play a contra-b (lowest b on a piano). "The Convalescent" acts as a reprise of the original motif, and ends with the entire orchestra climaxing on a massive chord.
"The Dance Song" features a very prominent violin solo throughout the section.
The end of the "Song of the Night Wanderer" leaves the piece half resolved, with high flutes, piccolos and violins playing a B major chord, while the lower strings pluck a C.
One of the major compositional themes of the piece is the contrast between the keys of B major, representing humanity, and C major, representing the universe. Because B and C are adjacent notes, these keys are tonally dissimilar: B major uses five sharps, while C major has none.