Reconstructing endoscopic videos is crucial for high-fidelity visualization and the efficiency of surgical operations. Despite the importance, existing 3D reconstruction methods encounter several challenges, including stringent demands for accuracy, imprecise camera positioning, intricate dynamic scenes, and the necessity for rapid reconstruction. Addressing these issues, this paper presents the first camera-pose-free scene reconstruction framework, Free-DyGS, tailored for dynamic surgical videos, leveraging 3D Gaussian splatting technology. Our approach employs a frame-by-frame reconstruction strategy and is delineated into four distinct phases: Scene Initialization, Joint Learning, Scene Expansion, and Retrospective Learning. We introduce a Generalizable Gaussians Parameterization module within the Scene Initialization and Expansion phases to proficiently generate Gaussian attributes for each pixel from the RGBD frames. The Joint Learning phase is crafted to concurrently deduce scene deformation and camera pose, facilitated by an innovative flexible deformation module. In the scene expansion stage, the Gaussian points gradually grow as the camera moves. The Retrospective Learning phase is dedicated to enhancing the precision of scene deformation through the reassessment of prior frames. The efficacy of the proposed Free-DyGS is substantiated through experiments on two datasets: the StereoMIS and Hamlyn datasets. The experimental outcomes underscore that Free-DyGS surpasses conventional baseline models in both rendering fidelity and computational efficiency.