We propose an efficient method for Hamiltonian simulation of multi-qubit quantum systems with special types of interaction. In our approach, the Hamiltonian of a \(n\)-qubit system should be represented as a linear combination of the standard Pauli basis operators, and then decomposed into a sum of partial Hamiltonians, which are, in general, not Pauli operators and satisfy some anticommutation relations. For three types of Hamiltonians, which are invariant with respect to permutations of qubits, the effectiveness of the main algorithm in the three-qubit cluster model is shown by calculating the operator exponentials for these Hamiltonians in an explicit analytical form. We also calculate the density operator, partition function, entropy, and free energy of the cluster weakly coupled to a thermal environment. In our model, the cluster is in the Gibbs state in the temperature interval \(0.1\!-\!2\:\!\text{K}\), which corresponds to the operating range of modern quantum processors. It follows from our analysis that the thermodynamic properties of such systems strongly depend on the type of internal interaction of qubits in the cluster.