In spintronics, transverse anomalous transport properties have emerged as a highly promising avenue surpassing the conventional longitudinal transport behaviors. Here, we explore the transverse transport properties of monolayer and bilayer Fe3−xCoxGaTe2 (x = 0.083, 0.167, 0.250, and 0.330) systems. All the systems exhibit ferromagnetic ground states with metallic features and also have perpendicular magnetic anisotropy. Besides, the magnetic anisotropy is substantially enhanced with increasing Co-doping concentration. However, unlike magnetic anisotropy, the Curie temperature is suppressed by increasing the Co-doping concentration. For instance, the monolayer and bilayer Fe2.917Co0.083GaTe2 hold a Curie temperature of 253 K and 269 K, which decreases to 163 K and 173 K in monolayer and bilayer Fe2.67Co0.33GaTe2 systems, respectively. We find a giant anomalous Nernst conductivity (ANC) of 6.03 A/(K·m) in the monolayer Fe2.917Co0.083GaTe2 at −30 meV, and this is further enhanced to 11.30 A/(K·m) in the bilayer Fe2.917Co0.083GaTe2 at −20 meV. Moreover, the bilayer Fe2.917Co0.083GaTe2 structure has a large anomalous thermal Hall conductivity (ATHC) of −0.14 W/(K·m) at 100 K. Overall, we find that the Fe3−xCoxGaTe2 (x = 0.083, 0.167, 0.250, and 0.330) structures have better anomalous transverse transport performance than the pristine Fe3GaTe2 system and can be used for potential spintronics and spin caloritronics applications.