Aiming to address dense small object tracking, we propose an image-to-trajectory framework including tracking and detection, where Track-Oriented Multiple Hypothesis Tracking(TOMHT) is revised for tracking. Unlike common cases of multi-object tracking, merged detections and the greater number of objects make dense small object tracking a more challenging problem. Firstly, we handle frequent merged detections through the aspects of detection and hypothesis selection. To tackle merged detection, we revise Local Contrast Method(LCM) and propose a multi-appearance variant, which exploits tree-like topological information and realizes one threshold for one object. Meanwhile, one-to-many constraint is employed via the proposed extended 0-1 programming, which enables hypothesis selection to handle track exclusions caused by merged detections. Secondly, to alleviate the high complexity caused by dense objects, we consider batch optimization and more rigorous and precise pruning technologies. Specifically, we propose autocorrelation based motion score test and two-stage hypotheses pruning. Experimental results are presented to verify the strength of our methods, which indicates speed and performance advantages of our tracker.