In the realm of practical problem-solving, multi-objective optimisation problems with redundant variables and indefinite objective functions (MOPRVIF) are becoming increasingly prevalent. MOPRVIF involve determining the optimal decision variables that optimise multiple objectives, leveraging the relational data of a set of variables and multiple objectives. For these problems, this paper focuses on the following two issues: one is the demand for a unified computational model to solve this problem; the other is how to improve the algorithm's deep intelligent search capability. In this regard,this paper designs a dual data-driven multi-objective optimisation method. The method used consisted of four parts: elimination of redundant variables (ERV), objective function construction (OFC), selection evolution operator (SEO), and multi-objective evolutionary algorithm (MOEA). MOEA was the main focus of the method. ERV is data preparation and variable selection according to multiple objectives. OFC involves constructing the relationship model between variables and objectives, and a high-accuracy model is important for guaranteeing reliable results. Furthermore, SEO can adjust the evolution operator during a deep search. This is an important guarantee for deep, intelligent search. MOEA combined OFC and SEO to form the final solution algorithm—Dual Data Driven Multi-Objective Evolutionary Algorithm (DDMOEA). DDMOEA was explored using two different disciplinary problems of drug compound optimisation and wild blueberry cultivation and benchmarks were selected. The first two problem domains are distinct. The first problem is more complex than the second; however, both encompass redundant variables and indefinite objective functions. Benchmarks are utilised independently to gauge the profound intelligent search capability. The experiments affirm that the dual data-driven optimization approach proposed in this paper is effective, practical, and scalable.