Traditionally, signal timing is done after the lane allocation. Recently, the lane-based optimisation is applied and considers the comprehensive optimisation of lane allocation and signal timing. In state-of-art lane-based design, only single layer, the entry into junction or exit from junction, is considered. This paper presents a lane-based model with second departing layer for estimating the reserved capacity of a signalised junction more accurately to resolve the overestimation of the capacity of an isolated junction. The two-layers are the stop-line layer and the link-approach interface. Via these layers, short-lane effect (SLE) can be easily modelled. Also, with the two-layer modelling, additional through lane design at junction can be modelled. New measure of effectiveness, the J-set degree of saturation, is proposed to describe the severity of SLE at flares. It can be shown that the problem can be solved by binary-mixed-integer linear programming (BMILP) method and numerical examples are demonstrated. Short cycles can even be generated, if it is better to do so, when the objective function is maximising reserve capacity.