Navigational conditions vary significantly across different inland waterway areas, making it difficult to standardize port equipment, navigation facilities, and transport organization. Therefore, unlocking the locational advantages and economic potentials of inland waterway transportation necessitates a new generation of waterborne transportation system (NEW-WTS) characterized by green and intelligent development. Moreover, research on planning tools for the NEW-WTS can provide a methodological basis for developing "one-region, one-scheme" solutions that support the green and intelligent transformation of diverse inland waterways. Based on a review of the fundamental theoretical system of the NEW-WTS, this study integrates the systems engineering methodology with the modular open systems approach (MOSA) and proposes a multilayer, progressively structured, and functionally closed-loop planning method for the NEW-WTS, namely the new generation of waterborne transportation system modular method (NEW-WTSMM). The construction logic of the NEW-WTSMM is elaborated from the perspectives of contents and procedures, models, and evaluation methods; in particular, the planning model is divided into four hierarchical layers: scenario classification, functional configuration, element implementation, and operational execution, covering the entire process from top-level design to engineering realization. Taking the Jining section of the Beijing ‒ Hangzhou Grand Canal as the application object, this study develops a NEW-WTS planning scheme for the port-to-port collaborative route between Longgong Port and Liangshan Port, and establishes a complete technical pathway encompassing top-level objective setting, subsystem functional-domain design, element-level logical composition, and unit-level operational mechanisms. The case results indicate that the NEW-WTSMM can support the technological integration of the NEW-WTS under complex inland waterway conditions, demonstrating engineering operability and adaptability to the commercial promotion of the NEW-WTS.