A bonding system comprising: a bonding apparatus including an activating apparatus (16,17) for irradiating a first substrate surface of a first substrate and a second substrate surface of a second substrate with particles, a thermometer for measuring the temperature of the first substrate or/and the temperature of the second substrate, a temperature adjusting device (52,54, 62, 64) for cooling or heating the first and/or the second substrate, and a pressure bonding mechanism for driving the second substrate and the first substrate so that the second substrate surface and the first substrate surface are in contact with each other; and a controller for controlling the bonding apparatus, wherein the controller includes an activating part arranged to control the activating apparatus (16,17) to irradiate the first substrate surface of a first substrate and the second substrate surface of a second substrate with particles to activate the substrate surfaces, a bonding part arranged to control the pressure bonding mechanism so that it drives the second substrate and the first substrate to bond the second substrate and the first substrate together after a temperature difference between the temperature of the first substrate and the temperature of the second substrate becomes equal to or lower than a predetermined value, characterised in that the bonding system further comprises a temperature adjusting part arranged to control the temperature adjusting device (52,54,62,64) to heat and/or cool the first substrate and/or the second substrate after an activating step and before bonding step based on the temperature measured by the thermometer so that the temperature of the first substrate surface and of the second substrate surface are in a predetermined range. a bonding apparatus including an activating apparatus (16,17) for irradiating a first substrate surface of a first substrate and a second substrate surface of a second substrate with particles, a thermometer for measuring the temperature of the first substrate or/and the temperature of the second substrate, a temperature adjusting device (52,54, 62, 64) for cooling or heating the first and/or the second substrate, and a pressure bonding mechanism for driving the second substrate and the first substrate so that the second substrate surface and the first substrate surface are in contact with each other; and a controller for controlling the bonding apparatus, wherein the controller includes an activating part arranged to control the activating apparatus (16,17) to irradiate the first substrate surface of a first substrate and the second substrate surface of a second substrate with particles to activate the substrate surfaces, a bonding part arranged to control the pressure bonding mechanism so that it drives the second substrate and the first substrate to bond the second substrate and the first substrate together after a temperature difference between the temperature of the first substrate and the temperature of the second substrate becomes equal to or lower than a predetermined value, characterised in that the bonding system further comprises a temperature adjusting part arranged to control the temperature adjusting device (52,54,62,64) to heat and/or cool the first substrate and/or the second substrate after an activating step and before bonding step based on the temperature measured by the thermometer so that the temperature of the first substrate surface and of the second substrate surface are in a predetermined range.