In ophthalmology, the use of femtosecond lasers is receiving more attention than ever due to its extremely high intensity and ultra short pulse duration. It opens the highly beneficial possibilities for minimized side effects during surgery process, and one of the specific areas is laser surgery in glaucoma treatment. However, the sophisticated femtosecond laser-ocular tissue interaction mechanism hampers the clinical application of femtosecond laser to treat glaucoma. The potential contribution in this work lies in the fact, that this is the first time a modified moving breakdown theory is applied, which is appropriate for femtosecond time scale, to analyze femtosecond laser-ocular tissue interaction mechanism. Based on this theory, energy deposition and corresponding thermal increase are studied by both simulation and experimentation. A simulation model was developed using Matlab software, and the simulation result was validated through in-vitro laser-tissue interaction experiment using pig iris. By comparing the theoretical and experimental results, it is shown that femtosecond laser can obtain determined ocular tissue removal, and the thermal damage is evidently reduced. This result provides a promising potential for femtosecond laser in glaucoma treatment.