The negative sign of the anomalous Nernst thermopower ($S_text{ANE}$) observed in Mn-Ga ordered alloys is an attractive property for thermoelectric applications exploiting the anomalous Nernst effect (ANE); however, its origin has not been clarified. In this study, to gain insight into the negative $S_text{ANE}$, we prepared epitaxial thin films of Mn$_{x}$Ga$_{100-x}$ with $x$ ranging from 56.2 to 71.7, and systematically investigated the structural, magnetic, and transport properties including the anomalous Hall effect (AHE) and the ANE. The measured $S_text{ANE}$ is negative for all samples and shows close to one order of magnitude difference among different compositions. Together with the measured transport properties, we were able to separate the two different contributions of the ANE, i.e., one originating from the transverse thermoelectric coefficient ($alpha_{xy}$), and the other one originating from the AHE acting on the longitudinal carrier flow induced by the Seebeck effect. Both contributions are found to be negative for all samples, while the experimentally obtained negative $alpha_{xy}$ exhibits a monotonic increase towards zero with increasing $x$, which is consistent with the tendency indicated by first-principles calculations. Our results show that the large difference in the negative $S_text{ANE}$ is mostly attributed to $alpha_{xy}$, and thus shed light on further enhancement of the ANE in Mn-based ordered alloys.