In this paper, we study the global existence and large-time behavior of strong solutions to the Cauchy problem of the one-dimensional isentropic compressible Navier-Stokes-Allen-Cahn system with phase field variable dependent viscosity, which models the motion of a mixture of two viscous compressible fluids. The case when the pressure p(ρ)=ργ, the viscosity ν(ρ,χ)=χα, the interface thickness δ(ρ)=ρβ and the relaxation time function a(ρ,χ,χy)=χλ is considered, where ρ>0 and χ are the density and the phase field variable, respectively, and γ,α,β,λ∈R are parameters. Under some conditions on the parameters γ,α,β,λ and the initial data, it is shown that the Cauchy problem of the one-dimensional isentropic compressible Navier-Stokes-Allen-Cahn system admits a unique global strong nonvacuum solution, which tends to the constant equilibrium state as time goes to infinity. Moreover, the exponential time decay rate of the phase field variable χ is also obtained. Here the initial perturbation for the phase field variable χ should be small, but the initial perturbations for the density and velocity of the fluid can be arbitrarily large.