According to the adsorption-desorption characteristics of coalbed gas and analysis of various experimental data, this paper proposes that the generation of secondary biogenic gas (SBG) and its mixing of with the residual thermogenic gas at an early stage inevitably lead to secondary changes of the thermogenic gas and various geochemical additive effects. Experimental results also show that the fractionation of the carbon isotope of methane of coal core desorption gas changes very little; the δ13C1 value of the mixed gas of biogenic and thermogenic gases is between the δ13C1 values of the two “original” gases, and the value is determined by the carbon isotopic compositions and mixing proportions of the two “original” methanes. Therefore this paper proposes that the study on the secondary changes of the thermogenic gas and various additive effects is a new effective way to study and identify SBG. Herein, a systematic example of research on the coalbed gas (Huainan coalbed gas) is further conducted, revealing a series of secondary changes and additive effects, the main characteristics and markers of which are: (1) the contents of CO2 and heavy-hydrocarbons decrease significantly; (2) the content of CH4 increases and the gas becomes drier; (3) the δ13C and δD values of methane decrease significantly and tend to have biogenetic characteristics; and (4) the values of δ13C2 and δ13CCO2 grow higher. These isotopic values also change with the degradation degrees by microbes and mixing proportions of the two kinds of gases in different locations. There exists a negative correlation between the δ13C1 vs δ13CCO2 values. The △δ13CC2–C1 values obviously become higher. The distributions of the △δ13CCO2–C1 values are within certain limits and show regularity. There exist a positive correlation between the N2 versus Ar contents, and a negative correlation between the N2 versus CH4 contents, indicating the down forward infiltration of the surface water containing air. These are important markers of the generation and existence of SBG.