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To improve the accuracy and effectiveness of continuous-time (CT) system identification, this paper introduces a novel method that incorporates the nuclear norm minimization (NNM) with the generalized Poisson moment functional (GPMF) based subspace method. The GPMF algorithm provides a simple linear mapping for subspace identification without the timederivatives of the input and output measurements to avoid amplification of measurement noise, and the NNM is a heuristic convex relaxation of the rank minimization. The Hankel matrix with minimized nuclear norm is used to determine the model order and to avoid the over-parameterization in subspace identification method (SIM). Furthermore, the algorithm to solve the NNM problem in CT case is also deduced with alternating direction methods of multipliers (ADMM). Lastly, two numerical examples are presented to evaluate the performance of the proposed method and to show the advantages of the proposed method over the existing methods.