As the basis of plant canopy chlorophyll fluorescence kinetics, light distribution within the canopy determines the interaction relationship between plant physical processes and ecological environment. Spectroscopy technology plays a very important role in building a prediction model of component content to plant canopies. However, there is only limited number of reports about chlorophyll fluorescence properties of different light intensity areas to free spindle apple canopies. In this paper, with the free spindle apple tree as the research object, the canopy space of apple tree was divided into five layers, and six cube grids with 50cm length of side in each layer, and then the light distribution was determined through measuring the light intensity of each cube grids space. firstly, spectrum data and characters of chlorophyll fluorescence were obtained in the different light area; secondly, a differential spectrum curve in red area(680~760 nm) was determined through removing the interference of system error by a differential spectrum; thirdly, relationship model has been established innovatively between the maximum value in red area(680~760 nm) and the chlorophyll fluorescence characters, which has been used as calculation method of chlorophyll fluorescence characters in different light area to apple tree canopy. Fourthly, root mean square error, mean absolute percentage error, mean forecast error were adopted to evaluate the method. The test result shows that the accuracy of the method is all above 80%, which can be the theoretical basis for pruning and getting best light distribution to apple tree canopy.