In our everyday experience termperature is due to the motion of atoms, molecules, etc. A neutron star, where protons and electrons are fused together to form neutrons, is nothing but a huge nucleus made up of neutrons. So, how does the concept of temperature arise?
Answer
First, strictly speaking a neutron star is not a nucleus since it is bound together by gravity rather than the strong force.
Measuring a surface temperature for any star is deceptively simple. All that is needed is a spectrum, which gives the luminous flux (or similar quantity) as a function of photon wavelength. There will be a broad thermal peak somewhere in the spectrum, whose peak wavelength can be converted to a temperature using Wien's displacement law:
$$T=\frac{b}{\lambda_{\rm max}}$$
with $b\sim2.9\times10^{-3}\rm mK^{-1}$. Neutron stars peak in the x-ray, and picking a wavelength of $1\;\rm nm$ (roughly in the middle of the logarithmic x-ray spectrum) gives a temperature of about $3$ million $\rm K$, which is in the ballpark of what is typically quoted for a neutron star.
More broadly than the motion of atoms or molecules, you can think of temperature as a measurement of the internal (not bulk) kinetic energy of a collection of particles, and energy is trivially related to temperature via Boltzmann's constant (though to get a more carefully defined concept of temperature requires a bit more work, see e.g. any derivation of Wien's displacement law).
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