It is an interesting issue if the transport behavior of a piezoelectric tunnel junction is sensitive to external strain or stress, and it implies a prospect for developing novel mechanical sensors, transducers, piezotronic devices, etc. Many studies paid attention to this issue, yet how the strain and stress tunable transport behavior of a tunnel junction depends on the barrier thickness is still rarely known. Using the first principles calculations, we investigate the size-dependent and strain-tunable transport behavior in the tunnel junctions. It was confirmed that external strain has strong control over the transport properties of ZnO tunnel junctions, with several times amplification of tunnel conductance obtained by strain reversal. More importantly, the conductance amplification by strain reversal exponentially changes with the barrier thickness, indicating the size-dependent strain tunability of the transport behavior. The electrostatic quantities (i.e., built-in field, depolarization field, polarization, interfacial dipoles and potential barrier) and the transport properties of tunnel junctions were comprehensively analyzed to reveal the relationships between these quantities and their size dependence. The exponential size-dependence of strain tunable transport behavior in ZnO tunnel junctions is attributed to the linear change in the potential barrier with the barrier thickness. Our simulations provide an insight of how to maximize the strain tunability of transport behavior of piezoelectric tunnel junctions by thickness design and strain engineering.