Biodiesel is a promising renewable alternative fuel, which can be used in diesel‐electric hybrid vehicles to potentially bring one kind of clean vehicle on the road. However, the fuel property variation can cause impacts to the powertrain and aftertreatment systems. In this paper, biodiesel's influence on post‐injection effects is studied. Experimental results are obtained to demonstrate the differences between diesel and biodiesel, and to build up fuel‐dependent maps of engine torque, temperature, and emissions. Utilizing those maps, an aftertreatment warm‐up approach compatible with both fuels is developed by strategically enabling double post injections. Finally, a supervisory controller based on model predictive control method is designed to optimize and balance the tradeoff between hybrid vehicle fuel economy and tailpipe emissions. Simulations are conducted for both fuels with or without the proposed control strategy. The validation results show that for both fuels, the controller can significantly reduce tailpipe emissions by successfully regulating the catalyst temperature to the desired range sacrificing fuel economy. And for biodiesel, additional fuel cost is required in order to realize the tradeoff.