The effect of parasitic ions on the results of ultraviolet A (UVA) cross-linking in iontophoresis was still not clear. In this work, the porcine sclera was cross-linked by riboflavin lactate Ringer’s solution (group A) and riboflavin normal saline (group B) in vitro, respectively. The concentration of parasitic ions in the solution was calculated. In addition, the average fluorescence intensity, penetration depth and concentration after the introduction of riboflavin and the mechanical properties of cross-linked sclera tissue were measured. The ranges of diffusion coefficient of the two solutions were also calculated, respectively. The results showed that more kinds of parasitic ions were detected in group A compared with group B, while the average fluorescence intensity, penetration depth and concentration of riboflavin and scleral elastic modulus in group B were significantly higher than those in group A when the penetration time was 10 minutes. Besides, the diffusion coefficient of riboflavin in group B was about 1.5 times larger than that in group A. The results suggested that the species of parasitic ions has a great impact on the permeability of riboflavin, and affects the mechanical properties of cross-linked sclera. The above results could provide a reference for improving the efficiency of riboflavin introduction and optimizing the formula of riboflavin in iontophoresis scleral cross-linking.