The invention discloses a method and a system for preprocessing MODIS (Moderate-Resolution Imaging Spectroradiometer) surface albedo data. The method comprises the following steps of: S1, acquiring remotely sensed data which are originally input; S2, carrying out missing data detection on the remotely sensed data which are originally input; S3, carrying out cloud and snow primary detection on theremotely sensed data which are originally input; S4, by using the obtained cloud and snow data as a training sample, detecting all data and identifying abnormal data; and S5, carrying out space-time filtering and interpolation on the remotely sensed data which are originally input. The system comprises a data input module, a data missing detection module, a cloud and snow detection module, an abnormal data detection module and a space-time filtering and interpolation module which are respectively used for implementing the above steps. According to the invention, by processing the missing and abnormal data in the surface albedo data, the surface albedo data of which a long-time sequence and space-time are continuously consistent can be generated and the accuracy of subsequent application and remote sensing inversion is improved.