PolyBin3D estimates the binned power spectrum and bispectrum for 3D fields such as the distributions of matter and galaxies. For each statistic, two estimators are available: the standard (ideal) estimators, which do not take into account the mask, and window-deconvolved estimators. In the second case, the computation of a Fisher matrix is required; this depends on binning and the mask, but does not need to be recomputed for each new simulation. PolyBin3D supports GPU acceleration using JAX. It is a sister code to PolyBin (ascl:2307.020), which computes the polyspectra of data on the two-sphere, and is a modern reimplementation of the former Spectra-Without-Windows (ascl:2108.011) code.