Blood constituent examination is an important means of health diagnosis. For blood constituent examination, we usually adopt the method of drawing blood, which bring pain and the risk of cross infection to the patient. Near infrared spectrum spectroscopy (NIRS) is a research hotspot in noninvasive blood constituent examination. The spectral data acquisition system of existing instruments is using a Single Chip Microcomputer (SCM) as its microcontroller. The spectral data acquisition system cannot realize the high speed multi-channel acquisition and storage of large amounts of data because of the SCM itself has certain deficiency. So a high speed multi-channel spectral data acquisition system based on Field Programmable Gate Array (FPGA) was designed in this paper in order to realize the system of high speed, multi-channel and high signal-to-noise ratio (SNR) in the area of noninvasive blood constituent examination by near infrared spectroscopy. An Altera Cyclone IV series FPGA was used as the microcontroller in this spectral data acquisition system, which simultaneously controlled two pieces of eight channels AD conversion chip acquiring 16 channels blood pulse wave signal parallel. Under the control of FPGA, the data was cached in FPGA internal ping-pong RAM first, after that it was transferred to an SRAM chip, finally it was sent to the computer via the USB port. Experiment result shows that the spectral data acquisition system can collect 16 channels signal parallel and fast under the sampling frequency of 19 531 Hz and the repetitive signal-to-noise ratio is over 40 000∶1. The system can collect 305 spectrograms per second, more over it can get high SNR human body blood pulse wave signal under the same circumstances. The spectral data acquisition system satisfies the basic requirements of the noninvasive blood constituent examination instrument by NIRS and it can make the instrument collect the human body blood pulse wave data at a high speed. The main innovation point of this article is applying FPGA to the spectral data acquisition system of near infrared noninvasive blood constituent examination instrument. FPGA is able to simultaneously control two pieces of eight channels AD conversion chip acquiring 16 channels blood pulse wave signal parallel. By using FPGA as the microcontroller of the spectral data acquisition system, we solve the problem that SCM as the microcontroller can’t realize multi-channel high speed data acquisition and storage of large amounts of data. The acquisition speed is greatly faster than the system before. The second innovation point of this article is we use FPGA internal resources establish a ping-pong RAM buffer. The spectral data from the AD chip is 24 bit, however, the SRAM chip has only 16 bit data bus. Via the ping-pang RAM buffer, the spectral data can transfer from AD chip to SRAM chip. The ping-pong RAM can realize different digits data seamless transfer from AD chip to SRAM chip.