The separation error caused by the Automatic Dependent Surveillance-Broadcast (ADS-B) positional uncertainty between two nearby aircrafts is studied in this paper. The condition when the separation error risk occurs is investigated based on the scenario of satellite navigation in civil aviation. To keep safe separation, many existing studies focused on the positional uncertainty quantification for a single aircraft using Global Navigation Satellite System (GNSS), for example, position accuracy and protection level (PL). Thus, correlation effect of uncertainties from multiple aircrafts is ignored. The present study demonstrates that the correlation effect is important for the separation risk evaluation involving two or more aircrafts. It is observed in this paper that the separation risk should be paid attention when two aircrafts are using different satellite-sets to navigate. A method is developed to evaluate an aircraft’s risk-probability of unsafe separation with an aircraft in the vicinity. The probability bound is calculated under the satellite fault hypotheses based on the conservative assumption of the aircraft using different satellite-sets with the target aircraft. Several simulation examples are used to illustrate the application of the proposed method for the risk evaluation in a time-varying environment at certain airspaces.