The invention provides an automatic tracking method and system applied to a space-based space target. The method includes the steps that an image including the space target needed to be tracked is collected; whether an automatic tracking task is executed for the first time or not is judged; if yes, the space target is detected and tracked, and a current second miss distance of the space target is calculated; if not, whether a tracking step executed in the process of automatic tracking is executed previously or not is judged; if yes, whether the number of continuous-losing times of space object tracking exceeds a preset threshold value of the number of losing times of space object tracking or not is judged, and if yes, the space object is detected again; if not, tracking is executed, and a current second miss distance of the space object is calculated; if the tracking step is not executed, the space object is detected again. The influences on the tracking process by a satellite dynamic base are eliminated, the requirement for automatically capturing and tracking the space object is met, when the target is located in a view field, the tracking state can be captured at once without forecasting the priori knowledge of the target through the ground, the method is reliable, miss distance calculation is precise, and the space-based tracking requirement is met.