This paper presents the flutter derivatives (FDs) extracted from a stochastic system identification (SSI) method under different turbulent flows. The objective of the study is to investigate the effects of oncoming turbulence on the flutter of suspended long-span bridges using a section model wind-tunnel test. Several wind-tunnel tests were performed on a truss bridge deck section with different oncoming turbulent properties involving reduced turbulence intensities and turbulent scales. This study includes an investigation of the effect of oncoming flows on modal dynamic responses. The transient and buffeting response data from the wind-tunnel test are analyzed using the system identification technique in extracting FDs, and the difficulties involved in this method are discussed. The time-domain SSI is applied to extract all FDs simultaneously from one and two degree-of-freedom (1DOF and 2DOF) systems. Finally, the results under different conditions are discussed and conclusions are formed.