In order to ensure the measurement precision of clock transition and accuracy of locking of 40Ca+ optical frequency standard,a method of multi-channel virtual pulse signal generation based on digital waveform of LabVIEW and data acquisition card was investigated. And the method benefits controlling automatically and conveniently the experimental process. The realized multi-channel generator adopts the way of multi-channel digital sequence sync-output and hardware clock of data acquisition card as timer. By programming the continuous rectangular pulses from the counter/timer,the output signals are sent to a data acquisition card as synchronous clock to control the output of digital waveform. The sample output rate of digital signal can reach 1 MHz,the precision of the pulse width can stably reach 1 μs and the rising delay is less than 50 ns. While all pulses of this generator are triggered simultaneously,the generator has good resolution,synchronism and stability.