To address the limitations of traditional data acquisition systems in air-to-air missile testing, such as insufficient multi-channel synchronous transmission, high-speed storage, and anti-interference capabilities, this study designs an anti-interference real-time data acquisition system based on the ZYNQ-7000 series and an EMMC 5-1-compliant storage module. The system enhances signal robustness through isolated LVDS interfaces and RS422 transceivers, achieves synchronous multi-source data acquisition via a tunable multi-channel sampling rate/baud rate architecture and hybrid framing technology, and ensures timing stability for high-speed EMMC read/write operations through dynamic calibration of data sampling points. Additionally, DDR3 cache is integrated to optimize burst data processing. Experimental results demonstrate that the single EMMC system achieves a write speed of 157.6 MB/s, a read speed of 180.1 MB/s, and a host computer data transmission rate of 40.78 Mb/s. By synergizing hardware isolation, framing optimization, and high-speed storage design, significantly enhancing real-time performance and anti-interference capabilities for multi-source data acquisition in high-dynamic environments. This system provides high-reliability data support for evaluating air-to-air missile performance.