A structure projection reconstruction method based on contrast transfer function correction of through-focus series of high-resolution transmission electron microscopy images is presented. In this method, defocus values are determined by evaluating phase similarities of the pixels on the Fourier transforms of the images after correction using trial defocus values. Two-fold astigmatism is also determined, by measuring focus variation along different directions. Each image in the series is corrected for the effects of contrast transfer function and then combined into a structure projection image. The method works for both crystalline and non-crystalline objects. Test results with experimental images are presented. Influences of experimental parameters for imaging and effects of crystal thickness on reconstruction are discussed.