The invention discloses a ship-lock multi-channel water level measuring system and a filter method thereof. The ship-lock multi-channel water level measuring system comprises a multi-water level sensor, a data acquisition module, a remote motoring PC (Personal Computer) machine, a GSM (Global System of Mobile communication) module, a communication network, and the like. The ship-lock multi-channel water level measuring system is characterized by monitoring the water levels of multiple measurement points, namely ship-lock upstream and downstream, a lock chamber, and the like, in real time by taking a singlechip as a lower microcontroller and using a high-accuracy A/D (Analog to Digital) convertor, packing and reforming multipath data and then remotely transmitting to an upper monitoring PC machine by utilizing a 485 bus to display the water level values of the measurement points in real time, transmitting water level information to a certain mobile phone subscriber through a GSM short message module and a wireless network thereof and supporting the mobile phone subscriber to actively take the water level values of the measurement points at any time by utilizing the GSM network. The ship-lock multi-channel water level measuring system disclosed by the invention is easy to realize the advantage of absolute stability by adopting an FIR (Finite Impulse Response) filter based on the median filter of the singlechip and has the advantages of low cost, high accuracy and anti-interference capacity and friendly human-computer interaction.