The invention discloses a small sized unmanned aerial vehicle based affected area estimating method, which comprises the following steps: based on a small sized unmanned aerial vehicle, performing image acquisition (S1); based on the surf characteristic point extraction, splicing and integrating the acquired images (S2); and based on the basic equipment parameters of the photographing equipment, calculating the resolution of the ground and according to the spliced and integrated image, estimating the actually affected area (S3). The invention further discloses a small sized unmanned aerial vehicle based affected area estimating system, comprising an image acquisition unit, a service platform and a computer. According to the technical schemes of the invention, a small sized four-rotor-wing unmanned aerial vehicle is used to acquire images of a protected land, which ensures the flexibility of image acquisition of the protected land and reduces the acquisition cost as well. The technical schemes also adopt the image matching and screening technology to construct a correlated image among the images and use the correlated image as the basis for the multi-band integration of the images. As a result, the overlapping regions in the image analyzing process can be effectively removed, and the estimating accuracy for the area of the protected land can be increased.