In this work, a deep Gaussian process (DGP) based framework is proposed to improve the accuracy of predicting flight trajectory in air traffic research, which is further applied to implement a probabilistic conflict detection algorithm. The Gaussian distribution is applied to serve as the probabilistic representation for illustrating the transition patterns of the flight trajectory, based on which a stochastic process is generated to build the temporal correlations among flight positions, i.e., Gaussian process (GP). Furthermore, to deal with the flight maneuverability of performing controller’s instructions, a hierarchical neural network architecture is proposed to improve the modeling representation for nonlinear features. Thanks to the intrinsic mechanism of the GP regression, the DGP model has the ability of predicting both the deterministic nominal flight trajectory (NFT) and its confidence interval (CI), denoting by the mean and standard deviation of the prediction sequence, respectively. The CI subjects to a Gaussian distribution, which lays the data foundation of the probabilistic conflict detection. Experimental results on real data show that the proposed trajectory prediction approach achieves higher prediction accuracy compared to other baselines. Moreover, the conflict detection approach is also validated by a obtaining lower false alarm and more prewarning time.