The top–down emission rate retrieval algorithm (TERRA) method for calculating the net flux out of a box has been employed by other researchers to assess large sources of methane release. This usually requires a manned aircraft drone with powerful performance to fly over the boundary layer. Few studies have focused on low-altitude box sampling mass balance methods for small sources of methane release, such as at maximum flight altitudes of less than 100 m. The accuracy and sources of uncertainty in such a method still need to be determined as they differ from the conditions of large sources. Nineteen flights were conducted to detect methane emissions from Chinese oil field well sites using a measurement system consisting of a quadcopter and methane, wind speed, wind direction, air pressure, and temperature sensors. The accuracy and uncertainty of the method are discussed. The average absolute relative error of the measurement is 18.5%, with an average uncertainty of 55.75%. The uncertainty is mainly caused by the wind speed and direction, and the background CH₄ concentration. The main paths to reduce uncertainty and improve accuracy for low-altitude box sampling include subtracting the background concentration during flux retrieval, enhancing the accuracy of methane measurements, selecting a period of downwind dominant or wind direction change of less than 30 degrees, and ensuring a maximum flight height greater than 50 m with a horizontal distance from the pollution source center of less than 75 m. The results show that TERRA-based low-altitude box sampling is suitable for quantifying methane release rates from small sources.