Methods for preparing conjugates including enzyme conjugates and especially alkaline phosphatase (ALP) conjugates, and a kit are provided. The methods include: blocking an amino group on a molecule surface of a first substance to be conjugated containing an amino group and a carboxyl group (for example, an enzyme) with a carboxyl compound; adding a carbodiimide to activate the first substance to be conjugated with the amino group blocked; inactivating or removing the carbodiimide; and adding a second substance containing an amino group (for example, a substance to be labeled). Conjugates (for example, enzyme conjugates) are obtained.