High volatile bituminous coal (HVBC) reservoirs are now regarded as one of the most important targets for coalbed methane (CBM) exploration and development in northwestern China. Water invasion during coalbed methane reservoir fracturing can induce water blockage damage, leading to decreased relative permeability of gas and reduced production of CBM well. To study the influences of heterogeneities of seepage pore and fracture on water invasion degree (WID), water flooding experiment using HVBC core was conducted to simulate water invasion; magnetic resonance imaging and gray calculation were applied to quantitatively determine WID; heterogeneous parameters of seepage pore and fracture were extracted based on micro-CT and fractal characterization; finally implications of seepage pore and fracture heterogeneities on WID were discussed, and water invasion mechanism was analyzed. The results show that fracture porosity, connected fracture porosity, minerals’ filling porosity, displacement pressure, efficiency of mercury withdrawal, and fractal dimension as well as tortuosity of seepage pore, are closely correlated with WID. As fracture porosity increases, WID initially increases then tends to be unchanged. Minerals’ filling can be dominated factor resisting water invasion when severe filling occurs. Seepage pores with good connection and permeability are beneficial for water invasion, while those with complex structure and tortuosity are detrimental to water invasion. Reservoirs developing connected fractures and homogeneous seepage pores are not only beneficial for water invasion, but also beneficial for water elimination. Reservoirs developing unconnected fractures and homogeneous seepage pores are beneficial for water invasion while detrimental to water elimination. Reservoirs lacking fractures’ development but developing complex structural seepage pores are detrimental to both water invasion and elimination.