To investigate higher harmonics induced by a submerged obstacle in the presence of uniform current, a 2D fully nonlinear numerical wave flume (NWF) is developed by use of a time-domain higher-order boundary element method (HOBEM) based on potential flow theory. A four-point method is developed to decompose higher bound and free harmonic waves propagating upstream and downstream around the obstacle. The model predictions are in good agreement with the experimental data for free harmonics induced by a submerged horizontal cylinder in the absence of currents. This serves as a benchmark to reveal the current effects on higher harmonic waves. The peak value of non-dimensional second free harmonic amplitude is shifted upstream for the opposing current relative to that for zero current with the variation of current-free incident wave amplitude, and it is vice versa for the following current. The second-order analysis shows a resonant behavior which is related to the ratio of the cylinder diameter to the second bound mode wavelength over the cylinder. The second-order resonant position slightly downshifted for the opposing current and upshifted for the following current.