The confocal fundus camera is a high-frame-rate scanning imaging system used for capturing detailed images of the fundus. However, during image acquisition, its fast-scanning mirror causes misalignment between odd and even scan lines in the reconstructed images. This misalignment happens due to a delay between the mirror's motion signals and the scanning rate signals. To resolve this issue, the study analyzed the relationship between the scanning time and the sampling time of the actual image height scanned by the galvanometer. By using an image similarity function based on normalized squared error, along with the Levenberg-Marquardt nonlinear least squares fitting algorithm, an effective correction of the odd-even row misalignment in the reconstructed image was developed. Additionally, this study introduces a new method for quantitatively assessing the degree of odd-even line misalignment in images. Experimental results demonstrate that the proposed correction algorithm can effectively prevent calibration failures caused by inaccurate feature extraction in traditional methods. This new correction method is versatile, working not only for confocal fundus cameras but also for other high-speed imaging systems. Moreover, the proposed evaluation method can sensitively reflect the degree of odd-even line misalignment in images. Images processed with the algorithm showed a 78.7234% improvement in horizontal resolution and a noticeable enhancement in overall clarity compared to uncorrected images.