We report an efficient method for fabrication of microfluidic chips with continuously changing cross-sections by a 3D bio-printer. The extruders of the printer are modified for melting sugar powder and printing liquid sugar with pneumatic driving. The material for printing is maltitol. Sacrificial sugar lines are firstly printed on a base polydimethylsiloxane (PDMS) layer and subsequently another PDMS layer is pouring onto it. After the PDMS is solidified, microfluidic chips are magnetically stirred in hot water to dissolve the sugar lines. The microfluidic chips are then already fabricated. Most importantly, to make the microfluidic chips own continuously changing cross-sections, we modify the G-code to let the printing speed change constantly. As speed slows down, diameter of the sugar filament would increase. Although some other parameters also have an effect on diameter of the microfluidic chips, the air pressure is hard to control and the temperature has a slow response. This fabrication method using 3D printing has high precision and repeatability. It is investigated that the microfluidic chips with channels down to 150μm have a margin of error of 3% compared with designed. Besides, the shape of the cross-sections of the microchannels is always like a circle, and the surface roughness is quite low.