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Abstract We study two dimensional systems with extended conformal symmetry generated by the W $$ \mathcal{W} $$ 3 algebra. These are expected to have an infinite number of commuting conserved charges, which we refer to as the quantum Boussinesq charges. We compute the eigenvalues of the quantum Boussinesq charges in both the vacuum and first excited states of the higher spin module through the ODE/IM correspondence. By studying the higher spin conformal field theory on the torus, we also calculate thermal correlators involving the energy-momentum tensor and the spin-3 current by making use of the Zhu recursion relations. By combining these results, we show that it is possible to derive the current densities, whose integrals are the quantum Boussinesq charges. We also evaluate the thermal expectation values of the conserved charges, and show that these are quasi-modular differential operators acting on the character of the higher spin module.