In this work, we propose a theory of temperature estimation of quantum systems, which is applicable in the regime of non-negligible prior temperature uncertainty and limited measurement data. In this regime the problem of establishing a well-defined measure of estimation precision becomes non-trivial, and furthermore the construction of a suitable criterion for optimal measurement design must be re-examined to account for the prior uncertainty. We propose a fully Bayesian approach to temperature estimation based on the concept of thermodynamic length, which solves both these problems. As an illustration of this framework, we consider thermal spin-$1/2$ particles and investigate the fundamental difference between two cases; on the one hand, when the spins are probing the temperature of a heat reservoir and, on the other, when the spins themselves constitute the sample.