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Frequency coding has been the traditional method implemented in steady-state visual evoked potential (SSVEP)-based brain-computer interfaces (BCI). However, it is limited in terms of possible target numbers and, consequently, inappropriate for certain applications involving liquid crystal display (LCD) with multiple stimuli. This paper proposes an innovative coding method for SSVEP that, through a combination of frequency and phase, increases the number of targets, thus it improves the information transfer rate (ITR). With this method, a BCI system with 15 targets was developed using three stimulus frequencies, which is five times as many targets as the traditional method. Additionally, this paper defines the concept of reference phase, and decodes the EEG by means of Fourier coefficient projections onto the reference phase directions. Through the optimization of lead position, reference phase, data segment length, and harmonic components, the average ITR exceeded 60 bits/min in a simulated online test with ten subjects.