In this study, fundamental questions in improving thermal efficiency of spark ignition engine were revisited, regarding two principal factors, i.e. stroke-to-bore ratio and valve timings. In our experiment, late intake valve closing (LIVC) Atkinson camshaft and various valve timing (VVT) module for valve timing control was equipped in the single cylinder, direct injection spark ignition (DISI) engine with 3 different stroke-to-bore ratios (1.00, 1.20 and 1.47). In these three setups, displacement and compression ratio were fixed. In addition, the tumble ratio for cylinder head was also kept the same to minimize the flow effect on the flame propagation caused by cylinder head, while to focus on the sole effect of changing the stroke-to-bore ratio. The experiments were performed in two steps; Firstly, univariate analysis based on the basic input variables - intake camshaft timing, exhaust camshaft timing and start of injection (SOI) - was conducted to understand the effect of each variable in various load conditions of each stroke-to-bore ratio. Secondly, design of experiment (DoE) was conducted to find the point of the optimum indicated thermal efficiency of each engine, considering the mutual effect among these input variables. The optimum results showed that at low load operation (IMEP 4.5 bar), the values of indicated efficiency are in the order of S/B ratio 1.20 > 1.00 > 1.47, mainly attributed by increased cooling and exhaust loss at higher S/B ratio (i.e. 1.47). However, in case of IMEP 6.5 bar, knock occurrence at lower S/B ratio (i.e. 1.00) led to retarded ignition timing, incurring higher exhaust loss and slower burning rate. In consequence, the best values of the net indicated fuel consumption (nisfc) at IMEP 6.5 bar are in the order of S/B ratio 1.20 > 1.47 > 1.00; 219.48 g/kWh at S/B ratio 1.20, 221.91 g/kWh at S/B ratio 1.47, and 222.51 g/kWh at S/B ratio 1.00.