In order to meet data acquisition mobility and convenient requirements of the portable ECG monitor, the data acquisition system of ECG with dual CPU is designed in this paper. The system, in which C8051F005 is master CPU, meanwhile ATmega168 is slave CPU, consists of analogical circuit for detecting of ECG, amplifier-filter circuit, A/D converter and SD memory card communication interface mainly. Experimental data shows that the system has such advantages such as good repeatability, high accuracy, quick response and excellent anti-interference. It can effectively detect and obtain electrical activity of the heart and cope with continuous large memory with SD memory card in embedded system. Strong background noises are eliminated effectively by multi-level amplifier and filter; Un-anamorphic ECG can be acquired and recorded synchronously in memory cards. Moreover, this paper also proposes a preprocessing algorithm for noise reduction so that it can reject the interference by respiration and surface EMG signal.