This paper extends the uniform design of a trunk-feeder system, e.g., rail-bus system, over a grid network in the literature to the heterogeneous design, where the spacings of feeder bus lines and stops are allowed to vary spatially to better serve the demand. The trunk lines are evenly deployed over the study area with the line spacing to be optimized. Employing the method of continuum approximation, we develop a joint design model to minimize the generalized system cost as a sum of transit patrons' cost, agency cost, and emission cost. The proposed model is applied on two types of trunk systems (i.e., rail and Bus Rapid Transit, BRT) in smalland large-sized city scenarios. The results indicate that: (i) the proposed model saves 31% of the system cost as compared with the uniform-designed feeder system; (ii) large-sized cities (e.g., New York City) prefer faster transit system as the trunk transit mode (i.e., rail), while small-sized cities welcome more economical trunk transit mode (i.e., BRT); and (iii) considering emission cost into the optimization model will lead to 9.43% reduction in actual emission cost.