The late-type spiral galaxy NGC 6946 is a prime example of molecular gas dynamics driven by ‘bars within bars’. Here, we use data from the BIMA Survey of Nearby Galaxies and HERA CO-Line Extragalactic Survey to analyse the structure and stability of its molecular disc. Our radial profiles exhibit a clear transition at distance R ∼ 1 kpc from the galaxy centre. In particular, the surface density profile breaks at R ≈ 0.8 kpc and is well fitted by a double exponential distribution with scalelengths R 1 ≈ 200 pc and R 2 ≈ 3 kpc, while the 1D velocity dispersion σ decreases steeply in the central kpc and is approximately constant at larger radii. The fact that we derive and use the full radial profile of σ rather than a constant value is perhaps the most novel feature of our stability analysis. We show that the profile of the Q stability parameter traced by CO emission is remarkably flat and well above unity, while the characteristic instability wavelength exhibits clear signatures of the nuclear starburst and inner bar within bar. We also show that CO-dark molecular gas, stars and other factors can play a significant role in the stability scenario of NGC 6946. Our results provide strong evidence that gravitational instability, radial inflow and disc heating have driven the formation of the inner structures and the dynamics of molecular gas in the central kpc.