When cooling towards a ferroelectric phase transition, collective atomic motions (phonons) slow down (soften) until a static atomic displacement pattern forms, giving rise to spontaneous polarization throughout the material1. However, in quantum paraelectrics such as strontium titanate (SrTiO3), long-range ferroelectric order does not develop at low temperatures due to persistent quantum fluctuations of ionic positions2,3. In SrTiO3, quantum paraelectricity emerges below Tq ≈ 40 K refs. 4–6 and is preceded by anomalous phonon dynamics: a transverse acoustic phonon mode partially softens at a finite wavevector, hinting at a modulated state at the nanoscale7–12. The precise real-space structure of SrTiO3 at low temperature, however, has remained unresolved despite decades of study. Here we directly image the low-temperature polar structure of a SrTiO3 lamella using cryogenic scanning transmission electron microscopy down to 20 K. High-resolution imaging reveals a spatially fluctuating landscape of nanoscale domains. Below about 105 K, short-range polar domains initially self-organize into a periodic structure extending over tens of nanometres; however, upon entering the quantum paraelectric regime below Tq, the process reverses and the periodically ordered polar nanodomains fragment into smaller clusters. Quantum paraelectricity in SrTiO3 underlies remarkable properties, including large dielectric permittivity13,14, proximity to ferroelectricity15,16, multiferroicity17 and unconventional superconductivity18–20. Our visualizations suggest that these phenomena may be linked to complex ordering and disordering of polar nanodomains at low temperature.