Brain computer interface is a control system between brain and outside devices by transforming electroencephalogram (EEG) signal. The brain computer interface system does not depend on the normal output pathways, such as peripheral nerve and muscle tissue, so it can provide a new way of the communication control for paralysis or nerve muscle damaged disabled persons. Steady state visual evoked potential (SSVEP) is one of non-invasive EEG signals, and it has been widely used in research in recent years. SSVEP is a kind of rhythmic brain activity simulated by continuous visual stimuli. SSVEP frequency is composed of a fixed visual stimulation frequency and its harmonic frequencies. The two-dimensional ensemble empirical mode decomposition (2D-EEMD) is an improved algorithm of the classical empirical mode decomposition (EMD) algorithm which extended the decomposition to two-dimensional direction. 2D-EEMD has been widely used in ocean hurricane, nuclear magnetic resonance imaging (MRI), Lena image and other related image processing fields. The present study shown in this paper initiatively applies 2D-EEMD to SSVEP. The decomposition, the 2-D picture of intrinsic mode function (IMF), can show the SSVEP frequency clearly. The SSVEP IMFs which had filtered noise and artifacts were mapped into the head picture to reflect the time changing trend of brain responding visual stimuli, and to reflect responding intension based on different brain regions. The results showed that the occipital region had the strongest response. Finally, this study used short-time Fourier transform (STFT) to detect SSVEP frequency of the 2D-EEMD reconstructed signal, and the accuracy rate increased by 16%.