To precisely address the critical issue of internal shot peening residue in slender tubes, which affects the service safety of high-end equipment, and to meet the stringent requirements for full-cycle quality assurance of core components in fields such as aerospace and precision medical devices, this study overcomes the limitations of existing nondestructive testing technologies. For the first time in the context of detecting shot peening residue inside slender tubes, this paper proposes combining eddy current testing technology with a lock-in amplifier and designs an integrated shot peening residue detection system based on field programmable gate array （FPGA） and a lock-in amplifier. Using an eddy current sensor as the probing tool, the system is inserted into the tube to capture the electromagnetic response generated by the residual shot. Based on cross-correlation theory, the lock-in amplifier enables precise extraction of weak phase signals. These signals are then quantified by a high-precision data acquisition module controlled by an FPGA, and finally, residue identification and location of the shot are achieved through phase variation characteristics. The system overcomes the application limitations of conventional ultrasonic testing, radiographic testing and single-mode eddy current testing. It can adapt to different detection scenarios through multi-frequency excitation, improving detection accuracy from the centimeter level to the millimeter level. It effectively detects residual shot of different sizes, requires no coupling agent and is unaffected by tube geometry or shot adhesion conditions. Additionally, the system offers fast detection speed, high efficiency, compact size, low cost, no radiation pollution, relaxed environmental requirements and ease of on-site deployment. A practical test platform was built to validate the detection of steel shot residue of various sizes inside aluminum-alloy slender tubes under different excitation frequencies. The results show that the detection system can effectively identify residual shots inside the tubes under different excitation frequencies. The average error in shot location detection is only 2.38 mm, with a standard deviation of 1.35 mm, and the signal-to-noise ratio is also improved compared to traditional eddy current testing methods.