Abstract: Deep coalbed methane (CBM) resources in the eastern margin of the Ordos Basin are abundant. However, significant variations in gas breakthrough time among production wells, coupled with a lack of targeted drainage system guidance and insufficient quantitative understanding of the relationship between free gas enrichment and the gas breakthrough process, constrain the efficient release of productivity. This study aims to elucidate the main controlling mechanisms of gas breakthrough time in deep CBM wells and establish an optimization method for drainage systems targeting shortened breakthrough time and enhanced productivity. Taking the northern eastern margin of the Ordos Basin as the study area, geological and production dynamic data from over a hundred wells were systematically collected. The concept of “gas appearance saturation” was proposed, and a quantitative calculation model integrating the gas state equation, Langmuir adsorption theory, and gas-water two-phase seepage mechanism was constructed, enabling the theoretical estimation of gas appearance saturation. Combined with experimental tests and production dynamic data, the coupling relationship between gas appearance saturation and the degree of free gas enrichment was analyzed. Furthermore, for the single-phase water drainage stage, drainage system optimization analysis was conducted using a combination of theoretical calculations and COMET3 numerical simulation. The results show that deep CBM wells exhibit three production modes: “gas appearance immediately upon opening the well” “gas appearance after short-term water drainage” and “gas appearance after long-term water drainage”. The gas breakthrough time distribution ranges from 0 to 276 days, with an average of 30.6 days. The breakthrough time is primarily controlled by the relative relationship between the initial free gas saturation and the gas appearance saturation, and is synergistically related to the average pressure drop rate and desorption efficiency before breakthrough. Theoretical calculations and numerical simulations indicate that the key to optimizing the drainage system during the single-phase water drainage stage for deep CBM wells lies in reasonably controlling the pressure drop rate. The reasonable pressure drop rate range for this stage in the study area is 0.10–0.25 MPa/d. Optimizing the drainage system for typical wells based on this range can shorten the gas breakthrough time by 8%–80% and increase the average daily gas production by 5.9%–11.8%. The concept of “gas appearance saturation” defined and the quantitative calculation model constructed in this study establish a quantitative link between the degree of free gas enrichment and the gas breakthrough time in deep coal seams. The proposed optimization method for the drainage system during the single-phase water drainage stage provides differentiated drainage technical strategies for deep, high-saturation CBM wells to achieve early gas breakthrough and enhanced productivity, offering theoretical support for the efficient development of deep coalbed methane.