According to the demands of mode-locked laser weak echo signal detection, a method which combined high-speed correlation sampling and parallel accumulation based on Field-Programmable Gate Array (FPGA) was proposed. This method overcame the shortcomings of the traditional sampling integral algorithm and can work real-timely without reference signal. Besides, a mode-locked laser weak echo signal detection system based on this method was designed and implemented. This system mainly consisted of a 12 bit@900 MSPS Analog-to-Digital Converter(ADC) chip, ADS5409, which sampled the echo signal and a FPGA chip, Kintex-7, which was in charge of controlling and on-line calculation. To the signal with the repetition frequency of 8 MHz and the average power of 0.04 nW, by accumulation of 16 000 pulses, this system can realize efficient detection and the calculation latency is shorter than 100 ns. In 900 experiments, the correct rate of the detection system reaches as high as 100% without false alarm.