In this work, the recent lattice Boltzmann (LB) model with self-tuning equationof state (EOS) [Huang et al., Phys. Rev. E 99, 023303 (2019)2470-004510.1103/PhysRevE.99.023303] is extended to three dimensions for the simulation of multiphase flows, which is based on the standard three-dimensional 27-velocity lattice and multiple-relaxation-time collision operator. To achieve the self-tuning EOS, the equilibrium moment is devised by introducing a built-in variable, and the collision matrix is improved by introducing some velocity-dependent nondiagonal elements. Meanwhile, the additional cubic terms of velocity in recovering the Newtonian viscous stress are eliminated to enhance the numerical accuracy. For modeling multiphase flows, an attractive pairwise interaction force is introduced to mimic the long-range molecular interaction, and a consistent scheme is proposed to compensate for the ɛ^{3}-order discrete lattice effect. Thermodynamic consistency in a strict sense is established for the multiphase LB model with self-tuning EOS, and the wetting condition is also treated in a thermodynamically consistent manner. As a result, the contact angle, surface tension, and interface thickness can be independently adjusted in the present theoretical framework. Numerical tests are first performed to validate the multiphase LB model with self-tuning EOS and the theoretical analyses of bulk and surface thermodynamics. The collision of equal-sized droplets is then simulated to demonstrate the applicability and effectiveness of the present LB model for multiphase flows.