This paper aims to present the inferences of the experimental studies on the performance, emission and combustion characteristics of Honge oil methyl ester (HOME) as a fuel for a single-cylinder direct injection diesel engine using response surface methodology (RSM) based mathematical modeling which are developed taking 27 set of experimental results. Experiments were carried out to study the effects of compression ratio, injection pressure and injection timing on performance characteristics like brake thermal efficiency (BTE), emissions such as smoke, hydrocarbon (HC), carbon monoxide (CO), nitric oxides (NOx) and combustion characteristics, namely, peak pressure and heat release rate (HRR) in a diesel engine using 3 and 4 hole injectors. The experiments were planned as per full factorial design (FFD) and RSM based quadratic models were developed to establish the relationships between the process parameters and the proposed characteristics. The response surface analysis based on the experimental results reveal that by retarding the injection timing (IT), increasing the injector-opening pressure (IOP) as well as the compression ratio would lead to increased BTE and reduced emissions. Increasing the number of nozzle holes improves the performance of diesel engine fueled with HOME in terms of increased BTE, reduced emissions like smoke, HC, CO and increased peak pressure and HRR. However, NOx emission increases with increased number of holes.