In recent years, the application prospect of urban logistics unmanned aerial vehicles has attracted extensive attention. The high-density operation of UAVs requires autonomous separation maintenance capability. To achieve autonomous separation maintenance, it is necessary to conduct autonomous track prediction and formulate the required separation accordingly. Based on the target level of safety requirements for UAV operation, aiming at the autonomous separation maintenance ability of UAVs and considering the accuracy of track prediction, a method to calculate the required separation between UAVs is proposed. This study consists of two parts. Firstly, based on historical data, the position prediction error of the flight track is investigated. Using a machine learning model, a two-stage track prediction method, which involves classification followed by prediction, is proposed for urban logistics UAV track data. Subsequently, based on the track prediction error distribution, by designing a gas model and a position error probability model, a separation-formulating model for urban logistics UAVs in free flight is proposed in which UAV maneuverability is considered. By applying this model, the required separation is formulated for UAVs. When the required separation is set to 48.5 m, the overall collision risk meets the TLS requirements. The research provides a feasible method for establishing autonomous separation for urban logistics UAVs.