Customised bus (CB) is a cutting-edge mean of transportation and has been implemented worldwide. To support the spread of the CB system, methodologies for CB network design have been conducted. However, a majority of them cannot be adopted directly for multi-modal transportation environment. In this paper, we proposed a bi-level programming model to fill this gap. The upper-level problem is to maximise the usage of the CB system with the limitation of operation constraints. Meanwhile, the lower-level problem is to capture the traveller’s choice by minimising traveller’s generalised cost during travel. A solving procedure via genetic algorithm is further proposed and validated via the metro data at Shanghai. The results indicated that the proposed CB route network would attract nearly 5,000 users during morning peak period under the given metro transaction data. We further studied the features of the selected routes and found that the CB network mainly served residence to commercial or industrial parks travellers and would provide travel service with fewer stops, and higher travel efficiency by travelling through expressway.