Laser tissue welding is a hot issue in surgical research due to its advantages of non-contact, instant water tightness, no suture removal, no rejection and anti-infection. However, the contradiction between strength and thermal damage has not been solved completely. The addition of dye can solve the problem. Therefore, in order to improve the welding strength and quality, this paper studies the influence of different position and concentration of dye on the welding strength and determines the optimal concentration and applied position. Two kinds of flux were prepared, which were based on bovine serum albumin solution and stained with indocyanine green and methylene blue respectively. Comparing the welding effect of flux, the indocyanine green group is more remarkable. When the concentration of indocyanine green is 2.0 mg/mL, the maximum tensile strength reaches 19.32 ± 1.22 N/cm2, which is significantly higher than that of the control group without flux. When the flux is applied to the front side, the tensile strength is higher than the reverse side group. Two kinds of flux can effectively reduce the thermal damage. Our study demonstrates that indocyanine green and methylene blue are significant organic chromophores in laser welding process, which can promote the efficiency of photo-thermal conversion, improve welding strength and reduce thermal damage.