The stretching of fluid elements combined with folding leads to a fluid dispersive property, which is an indicator of chaotic advection. A numerical calculation method was proposed for a dispersive property of the chaotic advection prescribed by a special structure. The effect of fluid dispersive property on heat transfer in a channel with orthogonal waves was analyzed, and the accuracy of numerical simulation was verified by performing a Laser Doppler Velocimetry experiment. The deformation of a material line along flow was studied. The streamlines are stretched and folded repeatedly, and the adjacent fluid particles are separated rapidly. Bigger degree of stretching and folding accelerates mixing of fluids with different temperatures and enhances heat transfer. Effect of geometric parameter on dispersive property was analyzed by designing an orthogonal experiment. The fluid dispersive exponents composed by stretching and folding between streamlines were calculated. The magnitude order of heat flux is completely according to the order of fluid dispersive exponent. Bigger fluid dispersive intensity enhances the ability of fluid carrying energy and results in bigger heat flux. The analysis and conclusions can be used to analyze chaotic intensity, which provides supplement for control of chaotic advection and design of chaotic structure.