Using nonequilibrium Green’s function method combined with density functional theory, we theoretically investigate the influences of alkaline and acid solutions on electronic transport properties in oligophenyleneethynylene molecular junctions with amino and carboxylic groups. The numerical results show that comparing with the case of neutral state, the conductance of the molecular junction is double improved and the rectifying direction is inverted when carboxylic group is deprotonated in the alkaline environment. On the other hand, the rectification ratio is enhanced trebly and the rectifying direction is inverted similarly when amino group is protonated in the acid environment. This theoretical work presents a chemically controllable method of manipulating conductance and rectification of molecular junctions.