A highly accurate, fast three-dimensional in vivo temperature mapping method is developed using MRI water photon chemical shift. It is important to have the precise temperature distribution information during laser-tissue thermal treatment. Several methods can be used for temperature measurement including thermal couple, optical fiber sensor, and MRI (magnetic resonance imaging) methods. MRI is the only feasible method for 3D in vivo, non-invasive temperature distribution measurement for laser-tissue interaction. The water proton chemical shift method is used in 3D MRI mapping. Varies MRI parameters, such as flip angle, TE, TR, spatial resolution, and temporal repetition, were optimized for the temperature mapping. The laser radiation of 805nm wavelength and a light-absorbing dye, indocyanine green (ICG) was used for temperature elevation. The measurement was conducted using gel phantom, chicken tissue and rats. The phantom system was constructed with a dye-enhanced spherical gel embedded in uniform gel phantom, simulating a tumor within normal tissue. The normal temperature elevation within ex vivo tissue such as chicken breast can reach up to 45-50 degree C with a power density of 1.3W/cm2 (with laser power of 3W and 1.7cm beam size). The temperature resolution is 0.37 degree C with a 0.2-mm spatial resolution and repetition rate of around 40 seconds. The external magnetic field drift effect is also evaluated.