Abstract The distribution of ejecta in young supernova remnants offers a powerful observational probe of their explosions and progenitors. Here we present a 3D reconstruction of the ejecta in SNR 0540-69.3, which is an O-rich remnant with a pulsar wind nebula located in the LMC. We use observations from the Very Large Telescope (VLT)/MUSE to study Hβ, [O iii] λ λ4959, 5007, Hα, [S ii] λ λ6717, 6731, [Ar iii] λ7136, and [S iii] λ9069. This is complemented by 2D spectra from VLT/X-shooter, which also cover [O ii] λ λ3726, 3729, and [Fe ii] λ12567. We identify three main emission components: (i) clumpy rings in the inner nebula (≲1000 km s⁻¹) with similar morphologies in all lines; (ii) faint extended [O iii] emission dominated by an irregular ring-like structure with radius ∼1600 km s⁻¹ and inclination ∼40°, but with maximal velocities reaching ∼3000 km s⁻¹; and (iii) a blob of Hα and Hβ located southeast of the pulsar at velocities ∼1500–3500 km s⁻¹. We analyze the geometry using a clump-finding algorithm and use the clumps in the [O iii] ring to estimate an age of 1146 ± 116 yr. The observations favor an interpretation of the [O iii] ring as ejecta, while the origin of the H-blob is more uncertain. An alternative explanation is that it is the blown-off envelope of a binary companion. From the detection of Balmer lines in the innermost ejecta we confirm that SNR 0540 was a Type II supernova and that hydrogen was mixed down to low velocities in the explosion.